https://launchpad.net/ubuntu/+source/openstructure/2.5.0-1ubuntu1/+build/27674365 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-077 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 Apr 13:57:36 ntpdate[1857]: adjust time server 10.211.37.1 offset 0.004963 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27674365 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27674365 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27674365 Starting target for build PACKAGEBUILD-27674365 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27674365 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27674365 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27674365 Updating target for build PACKAGEBUILD-27674365 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1407 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6097 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main arm64 Packages [694 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe arm64 Packages [4630 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [640 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [228 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4092 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1562 kB] Fetched 37.4 MB in 8s (4646 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 159 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 77.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl-dev arm64 1.3.0-3build3 [72.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu8 [1596 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu8 [19.7 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1build1 [201 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libnss-nisplus arm64 1.3-5build1 [22.5 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1build1 [83.6 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgssapi-krb5-2 arm64 1.20.1-6ubuntu2 [141 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5-3 arm64 1.20.1-6ubuntu2 [349 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libk5crypto3 arm64 1.20.1-6ubuntu2 [85.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5support0 arm64 1.20.1-6ubuntu2 [33.9 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.2-1 [17.0 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapparmor1 arm64 4.0.0-beta3-0ubuntu3 [50.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcap-ng0 arm64 0.8.4-2build2 [14.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit1 arm64 1:3.1.2-2.1build1 [47.6 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libblkid1 arm64 2.39.3-9ubuntu4 [123 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu1 [30.1 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.6.1+really5.4.5-1 [125 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkmod2 arm64 31+20240202-2ubuntu5 [51.6 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libselinux1 arm64 3.5-2ubuntu2 [79.9 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmount1 arm64 2.39.3-9ubuntu4 [133 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-6build1 [721 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1build1 [34.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1build1 [6578 B] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2build1 [4773 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2build1 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2build1 [1777 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu5 [15.3 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build3 [13.1 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-charwidth-perl arm64 0.04-11build3 [9406 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6 arm64 2.39-0ubuntu8 [2774 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-bin arm64 2.39-0ubuntu8 [591 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu3 [984 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.4-1ubuntu6 [2016 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu3 [262 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu3 [1793 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.4-1ubuntu6 [104 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.4-1ubuntu6 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.4-1ubuntu6 [3403 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.4-1ubuntu6 [424 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu4 [50.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules arm64 1.5.3-5ubuntu4 [278 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2build1 [192 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2build1 [199 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu1 [275 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu3 [942 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapt-pkg6.0t64 arm64 2.7.14build2 [935 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bzip2 arm64 1.0.8-5.1 [34.0 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbz2-1.0 arm64 1.0.8-5.1 [35.7 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-14-base arm64 14-20240330-1ubuntu2 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-s1 arm64 14-20240330-1ubuntu2 [50.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++6 arm64 14-20240330-1ubuntu2 [748 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.4-1ubuntu6 [173 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu2 [61.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.6-1 [22.6 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2 [67.1 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebconfclient0 arm64 0.271ubuntu3 [11.3 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu2 [703 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg arm64 2.4.4-2ubuntu16 [548 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-4build1 [153 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-4build1 [56.5 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu1 [146 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu1 [104 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg-agent arm64 2.4.4-2ubuntu16 [221 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgconf arm64 2.4.4-2ubuntu16 [103 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 pinentry-curses arm64 1.2.1-3ubuntu5 [34.3 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnpth0t64 arm64 1.6-3.1build1 [8144 B] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgv arm64 2.4.4-2ubuntu16 [150 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libseccomp2 arm64 2.5.5-1ubuntu3 [51.1 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt-utils arm64 2.7.14build2 [205 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt arm64 2.7.14build2 [1336 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 debconf-i18n all 1.5.86 [205 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 debconf all 1.5.86 [124 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam0g arm64 1.5.3-5ubuntu4 [67.7 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu3 [128 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libuuid1 arm64 2.39.3-9ubuntu4 [35.3 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfdisk1 arm64 2.39.3-9ubuntu4 [142 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 mount arm64 2.39.3-9ubuntu4 [116 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu3 [22.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3 [9550 B] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl2 arm64 1.3.0-3build3 [41.6 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-20.20 [1570 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 base-files arm64 13ubuntu9 [73.9 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debianutils arm64 5.17build1 [90.2 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bash arm64 5.2.21-2ubuntu4 [780 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdutils arm64 1:2.39.3-9ubuntu4 [97.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 coreutils arm64 9.4-3ubuntu5 [1362 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.6ubuntu6 [1265 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 dash arm64 0.5.12-6ubuntu5 [90.4 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu2 [97.1 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 hostname arm64 3.23+nmu2ubuntu1 [10.9 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu1 [200 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu1 [186 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 util-linux arm64 2.39.3-9ubuntu4 [1114 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu2 [33.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu3 [22.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu3 [225 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu3 [594 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 optipng arm64 0.7.8+ds-1build2 [109 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-5build1 [185 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu4 [64.3 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 uuid-runtime arm64 2.39.3-9ubuntu4 [32.5 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage2 arm64 3.5-1build5 [90.8 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu1 [838 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu3 [58.5 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu3 [16.5 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1 [124 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 procps arm64 2:4.0.4-4ubuntu3 [708 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdextrautils arm64 2.39.3-9ubuntu4 [71.5 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgpm2 arm64 1.20.7-11 [14.7 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu1 [23.3 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libjansson4 arm64 2.14-2build2 [34.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.7-1build1 [178 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.6.1+really5.4.5-1 [268 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-4ubuntu2 [777 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-4ubuntu2 [95.7 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-4ubuntu2 [99.8 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-4ubuntu2 [3291 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-4ubuntu2 [767 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-4ubuntu2 [18.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-4ubuntu2 [239 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-4ubuntu2 [14.4 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240330-1ubuntu2 [1151 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13 arm64 13.2.0-23ubuntu3 [14.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu3 [2378 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240330-1ubuntu2 [144 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240330-1ubuntu2 [27.9 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240330-1ubuntu2 [11.4 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240330-1ubuntu2 [2920 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240330-1ubuntu2 [1282 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240330-1ubuntu2 [1599 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13 arm64 13.2.0-23ubuntu3 [469 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu3 [2468 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240330-1ubuntu2 [2688 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240330-1ubuntu2 [44.7 kB] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13 arm64 13.2.0-23ubuntu3 [1030 B] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-base arm64 13.2.0-23ubuntu3 [48.7 kB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [20.1 MB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [11.7 MB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [10.3 MB] Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Preconfiguring packages ... 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Unpacking systemd (255.4-1ubuntu6) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu6_arm64.deb ... 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Setting up libgcc-13-dev:arm64 (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:arm64 (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1build1) ... Setting up binutils-aarch64-linux-gnu (2.42-4ubuntu2) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3build3) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:arm64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:arm64 (1.3.0-3build3) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15848 files and directories currently installed.) Purging configuration files for libssl3:arm64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27674365 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27674365 --arch=arm64 --dist=noble-proposed --nolog openstructure_2.5.0-1ubuntu1.dsc Initiating build PACKAGEBUILD-27674365 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-077.buildd +==============================================================================+ | openstructure 2.5.0-1ubuntu1 (arm64) Wed, 03 Apr 2024 13:58:57 +0000 | +==============================================================================+ Package: openstructure Version: 2.5.0-1ubuntu1 Source Version: 2.5.0-1ubuntu1 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27674365/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/openstructure-9LKCv1/resolver-KKCYh7' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- openstructure_2.5.0-1ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/openstructure-9LKCv1/openstructure-2.5.0' with '<>' I: NOTICE: Log filtering will replace 'build/openstructure-9LKCv1' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev, libopenmm-plugins, libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib, python3-numpy, python3-pil, python3-pyqt5, python3-scipy, qtbase5-dev, sip-dev, voronota, build-essential, fakeroot Filtered Build-Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev, libopenmm-plugins, libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib, python3-numpy, python3-pil, python3-pyqt5, python3-scipy, qtbase5-dev, sip-dev, voronota, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [960 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [542 B] Get:5 copy:/<>/apt_archive ./ Packages [588 B] Fetched 2090 B in 0s (77.7 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev blt clustalw cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dssp dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gettext gettext-base gfortran-13 gfortran-13-aarch64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcifpp-data libcifpp5 libcups2t64 libcurl4t64 libdbus-1-3 libdebhelper-perl libdeflate-dev libdeflate0 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libegl-dev libegl-mesa0 libegl1 libeigen3-dev libelf1t64 libevdev2 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgfortran-13-dev libgfortran5 libgl-dev libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglu1-mesa libglu1-mesa-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgraphite2-3 libgudev-1.0-0 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libice6 libicu-dev libicu74 libimagequant0 libinput-bin libinput10 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc-dev liblerc4 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmd4c0 libmtdev1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopengl-dev libopengl0 libopenjp2-7 libopenmm-dev libopenmm-plugins libopenmm8.0t64 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpcre2-16-0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpng-dev libpsl5t64 libpthread-stubs0-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5concurrent5t64 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5-dev libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libraqm0 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv-dev libsharpyuv0 libsm6 libsqlite3-dev libssh-4 libsub-override-perl libtcl8.6 libtiff-dev libtiff6 libtiffxx6 libtk8.6 libtool libuchardet0 libucx0 libuv1t64 libvulkan-dev libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-server0 libwebp-dev libwebp7 libwebpdecoder3 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxft2 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxxf86vm1 libzstd-dev m4 man-db media-types mpi-default-bin mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf python-matplotlib-data python3 python3-appdirs python3-attr python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-fonttools python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-pyqt5 python3-pyqt5.sip python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12 python3.12-dev python3.12-minimal qt5-qmake qt5-qmake-bin qtbase5-dev qtbase5-dev-tools qtchooser shared-mime-info sip-dev tk8.6-blt2.5 unicode-data voronota x11-common x11proto-dev xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-doc libcoarrays-dev groff lrzip libboost-doc graphviz libboost1.83-doc gccxml libboost-contract1.83-dev libmpfrc++-dev libntl-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop cups-common libeigen3-doc libfftw3-doc low-memory-monitor icu-doc libjs-jquery-ui-docs liblcms2-utils libtool-doc liblzma-doc openmpi-doc pciutils libthai0 qgnomeplatform-qt5 qt5-image-formats-plugins lm-sensors sqlite3-doc tcl8.6 tk8.6 gcj-jdk libwacom-bin libx11-doc libxcb-doc libxext-doc m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc python3-venv python-attr-doc python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python3-pytest python-pil-doc python-pyparsing-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.12-venv python3.12-doc binfmt-support default-libmysqlclient-dev firebird-dev libpq-dev unixodbc-dev python-sip-doc Recommended packages: curl | wget | lynx dbus libarchive-cpio-perl libgl1-amber-dri libglib2.0-data xdg-user-dirs javascript-common libldap-common libcoarrays-openmpi-dev libpng-tools publicsuffix qttranslations5-l10n libqt5svg5 qt5-gtk-platformtheme qtwayland5 libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc | libqt5sql5-psql | libqt5sql5-tds | libqt5sql5-ibase libsasl2-modules mesa-vulkan-drivers | vulkan-icd xauth libmail-sendmail-perl python3-bs4 python3-cssselect python3-html5lib python3-olefile isympy-common python3-sip-dev The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt clustalw cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dssp dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gettext gettext-base gfortran-13 gfortran-13-aarch64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcifpp-data libcifpp5 libcups2t64 libcurl4t64 libdbus-1-3 libdebhelper-perl libdeflate-dev libdeflate0 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1t64 libedit2 libegl-dev libegl-mesa0 libegl1 libeigen3-dev libelf1t64 libevdev2 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libexpat1-dev libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgfortran-13-dev libgfortran5 libgl-dev libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglu1-mesa libglu1-mesa-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgraphite2-3 libgudev-1.0-0 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libice6 libicu-dev libicu74 libimagequant0 libinput-bin libinput10 libjbig-dev libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc-dev liblerc4 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmd4c0 libmtdev1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopengl-dev libopengl0 libopenjp2-7 libopenmm-dev libopenmm-plugins libopenmm8.0t64 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpcre2-16-0 libpipeline1 libpkgconf3 libpmix-dev libpmix2t64 libpng-dev libpsl5t64 libpthread-stubs0-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5concurrent5t64 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5-dev libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libraqm0 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv-dev libsharpyuv0 libsm6 libsqlite3-dev libssh-4 libsub-override-perl libtcl8.6 libtiff-dev libtiff6 libtiffxx6 libtk8.6 libtool libuchardet0 libucx0 libuv1t64 libvulkan-dev libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-server0 libwebp-dev libwebp7 libwebpdecoder3 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxft2 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxnvctrl0 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxxf86vm1 libzstd-dev m4 man-db media-types mpi-default-bin mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf python-matplotlib-data python3 python3-appdirs python3-attr python3-brotli python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-fonttools python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-pyqt5 python3-pyqt5.sip python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12 python3.12-dev python3.12-minimal qt5-qmake qt5-qmake-bin qtbase5-dev qtbase5-dev-tools qtchooser sbuild-build-depends-main-dummy shared-mime-info sip-dev tk8.6-blt2.5 unicode-data voronota x11-common x11proto-dev xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 430 newly installed, 0 to remove and 0 not upgraded. Need to get 276 MB of archives. After this operation, 1427 MB of additional disk space will be used. 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libpython3-stdlib arm64 3.12.2-0ubuntu2 [9854 B] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3 arm64 3.12.2-0ubuntu2 [24.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbsd0 arm64 0.12.1-1build1 [40.9 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdbus-1-3 arm64 1.14.10-4ubuntu3 [210 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libelf1t64 arm64 0.190-1.1build3 [58.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfribidi0 arm64 1.0.13-3 [26.5 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.80.0-6ubuntu1 [1289 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libicu74 arm64 74.2-1ubuntu1 [10.8 MB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxml2 arm64 2.9.14+dfsg-1.3ubuntu3 [735 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 shared-mime-info arm64 2.4-4 [472 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 xkb-data all 2.41-2 [395 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic-mgc arm64 1:5.45-3build1 [307 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic1t64 arm64 1:5.45-3build1 [85.7 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 file arm64 1:5.45-3build1 [22.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gettext-base arm64 0.21-14ubuntu1 [37.5 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libuchardet0 arm64 0.0.8-1 [75.1 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 groff-base arm64 1.23.0-3build2 [993 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libcbor0.10 arm64 0.10.2-1.2ubuntu2 [26.0 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-common all 2.4.120-2 [7998 B] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm2 arm64 2.4.120-2 [42.1 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libedit2 arm64 3.1-20230828-1 [96.4 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfido2-1 arm64 1.14.0-1build2 [82.5 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnghttp2-14 arm64 1.59.0-1build2 [74.0 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpipeline1 arm64 1.5.7-2 [23.7 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1build1 [57.4 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libuv1t64 arm64 1.48.0-1.1build1 [95.3 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxau6 arm64 1:1.0.9-1build5 [7624 B] Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu5 [10.8 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1 arm64 1.15-1 [47.6 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-data all 2:1.8.7-1 [115 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-6 arm64 2:1.8.7-1 [645 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxext6 arm64 2:1.3.4-1build1 [31.1 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 man-db arm64 2.12.0-4build1 [1232 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssh-client arm64 1:9.6p1-3ubuntu12 [884 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbrotli1 arm64 1.1.0-2build2 [339 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfreetype6 arm64 2.13.2+dfsg-1build3 [393 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 clustalw arm64 2.1+lgpl-7 [240 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libarchive13t64 arm64 3.7.2-2 [376 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-5ubuntu2 [21.4 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-5ubuntu2 [54.7 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libldap2 arm64 2.6.7+dfsg-1~exp1ubuntu7 [193 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build7 [57.8 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssh-4 arm64 0.10.6-2build2 [189 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu9 [333 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjsoncpp25 arm64 1.9.5-6 [76.0 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 librhash0 arm64 1.4.3-3 [125 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cmake-data all 3.28.3-1build6 [2155 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cmake arm64 3.28.3-1build6 [10.3 MB] Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdw1t64 arm64 0.190-1.1build3 [258 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debugedit arm64 1:5.0-5build1 [45.4 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dwz arm64 0.15-1build6 [113 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 debhelper all 13.14.1ubuntu5 [869 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 dh-python all 6.20240401 [110 kB] Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 libcifpp-data all 5.0.7.1-3build1 [450 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 libcifpp5 arm64 5.0.7.1-3build1 [867 kB] Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 dssp arm64 4.2.2-2 [659 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 fonts-lyx all 2.4.0~RC3-1build3 [171 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240330-1ubuntu2 [443 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgfortran-13-dev arm64 13.2.0-23ubuntu3 [478 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [10.8 MB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gfortran-13 arm64 13.2.0-23ubuntu3 [10.9 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-200 arm64 3.7.0-0.3 [57.3 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [182 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libibverbs1 arm64 50.0-2build2 [67.3 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ibverbs-providers arm64 50.0-2build2 [367 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libllvm17t64 arm64 1:17.0.6-9build3 [25.0 MB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libavahi-common-data arm64 0.8-13ubuntu5 [29.6 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libavahi-common3 arm64 0.8-13ubuntu5 [23.3 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libavahi-client3 arm64 0.8-13ubuntu5 [27.2 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost1.83-dev arm64 1.83.0-2.1ubuntu3 [10.7 MB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-dev arm64 1.83.0.1ubuntu2 [4308 B] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost1.83-tools-dev arm64 1.83.0-2.1ubuntu3 [1363 kB] Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-tools-dev arm64 1.83.0.1ubuntu2 [4238 B] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-atomic1.83.0 arm64 1.83.0-2.1ubuntu3 [239 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-atomic1.83-dev arm64 1.83.0-2.1ubuntu3 [235 kB] Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-atomic-dev arm64 1.83.0.1ubuntu2 [4358 B] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-2.1ubuntu3 [244 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-chrono1.83-dev arm64 1.83.0-2.1ubuntu3 [245 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-chrono-dev arm64 1.83.0.1ubuntu2 [4672 B] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-container1.83.0 arm64 1.83.0-2.1ubuntu3 [261 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-container1.83-dev arm64 1.83.0-2.1ubuntu3 [270 kB] Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-container-dev arm64 1.83.0.1ubuntu2 [4530 B] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-date-time1.83.0 arm64 1.83.0-2.1ubuntu3 [236 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-serialization1.83.0 arm64 1.83.0-2.1ubuntu3 [335 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-serialization1.83-dev arm64 1.83.0-2.1ubuntu3 [392 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-date-time1.83-dev arm64 1.83.0-2.1ubuntu3 [239 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-system1.83.0 arm64 1.83.0-2.1ubuntu3 [236 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-system1.83-dev arm64 1.83.0-2.1ubuntu3 [231 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-thread1.83.0 arm64 1.83.0-2.1ubuntu3 [275 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-thread1.83-dev arm64 1.83.0-2.1ubuntu3 [284 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-context1.83.0 arm64 1.83.0-2.1ubuntu3 [237 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-context1.83-dev arm64 1.83.0-2.1ubuntu3 [232 kB] Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-context-dev arm64 1.83.0.1ubuntu2 [4276 B] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-coroutine1.83.0 arm64 1.83.0-2.1ubuntu3 [234 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-coroutine1.83-dev arm64 1.83.0-2.1ubuntu3 [237 kB] Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-coroutine-dev arm64 1.83.0.1ubuntu2 [4342 B] Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-date-time-dev arm64 1.83.0.1ubuntu2 [4058 B] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-exception1.83-dev arm64 1.83.0-2.1ubuntu3 [230 kB] Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-exception-dev arm64 1.83.0.1ubuntu2 [4058 B] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2.1ubuntu3 [281 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-filesystem1.83-dev arm64 1.83.0-2.1ubuntu3 [301 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-fiber1.83.0 arm64 1.83.0-2.1ubuntu3 [255 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-fiber1.83-dev arm64 1.83.0-2.1ubuntu3 [270 kB] Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-fiber-dev arm64 1.83.0.1ubuntu2 [4486 B] Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-filesystem-dev arm64 1.83.0.1ubuntu2 [4094 B] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph1.83.0 arm64 1.83.0-2.1ubuntu3 [354 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-regex1.83.0 arm64 1.83.0-2.1ubuntu3 [329 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-regex1.83-dev arm64 1.83.0-2.1ubuntu3 [349 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-test1.83.0 arm64 1.83.0-2.1ubuntu3 [444 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-test1.83-dev arm64 1.83.0-2.1ubuntu3 [572 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph1.83-dev arm64 1.83.0-2.1ubuntu3 [397 kB] Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-graph-dev arm64 1.83.0.1ubuntu2 [4160 B] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [90.3 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [7932 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 librdmacm1t64 arm64 50.0-2build2 [70.6 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libfabric1 arm64 1.17.0-3build2 [541 kB] Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmunge2 arm64 0.5.15-4build1 [14.9 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix2t64 arm64 5.0.1-4.1build1 [655 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libucx0 arm64 1.16.0+ds-4build1 [1076 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi3t64 arm64 4.1.6-7ubuntu2 [2463 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi1.83.0 arm64 1.83.0-2.1ubuntu3 [269 kB] Get:175 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph-parallel1.83.0 arm64 1.83.0-2.1ubuntu3 [276 kB] Get:176 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph-parallel1.83-dev arm64 1.83.0-2.1ubuntu3 [291 kB] Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-graph-parallel-dev arm64 1.83.0.1ubuntu2 [4192 B] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2.1ubuntu3 [258 kB] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-iostreams1.83-dev arm64 1.83.0-2.1ubuntu3 [265 kB] Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-iostreams-dev arm64 1.83.0.1ubuntu2 [4046 B] Get:181 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-json1.83.0 arm64 1.83.0-2.1ubuntu3 [365 kB] Get:182 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-json1.83-dev arm64 1.83.0-2.1ubuntu3 [387 kB] Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-json-dev arm64 1.83.0.1ubuntu2 [4172 B] Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-locale1.83.0 arm64 1.83.0-2.1ubuntu3 [404 kB] Get:185 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-locale1.83-dev arm64 1.83.0-2.1ubuntu3 [587 kB] Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-locale-dev arm64 1.83.0.1ubuntu2 [4378 B] Get:187 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-log1.83.0 arm64 1.83.0-2.1ubuntu3 [654 kB] Get:188 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-log1.83-dev arm64 1.83.0-2.1ubuntu3 [945 kB] Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-log-dev arm64 1.83.0.1ubuntu2 [4260 B] Get:190 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-math1.83.0 arm64 1.83.0-2.1ubuntu3 [431 kB] Get:191 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-math1.83-dev arm64 1.83.0-2.1ubuntu3 [573 kB] Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-math-dev arm64 1.83.0.1ubuntu2 [4264 B] Get:193 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-common all 4.1.6-7ubuntu2 [170 kB] Get:194 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-dev arm64 3.7.0-0.3 [105 kB] Get:195 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [225 kB] Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libibverbs-dev arm64 50.0-2build2 [686 kB] Get:197 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma-dev arm64 2.0.18-1 [39.5 kB] Get:198 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl7 arm64 2.4.7-7 [40.3 kB] Get:199 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl-dev arm64 2.4.7-7 [170 kB] Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-dev arm64 2.10.0-1 [259 kB] Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [140 kB] Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [62.1 kB] Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-9ubuntu2 [14.7 kB] Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-dev arm64 2.1.12-stable-9ubuntu2 [283 kB] Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Get:206 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix-dev arm64 5.0.1-4.1build1 [4022 kB] Get:207 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:209 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-bin arm64 4.1.6-7ubuntu2 [113 kB] Get:210 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi-dev arm64 4.1.6-7ubuntu2 [865 kB] Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-dev arm64 1.15 [3118 B] Get:212 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi1.83-dev arm64 1.83.0-2.1ubuntu3 [299 kB] Get:213 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-mpi-dev arm64 1.83.0.1ubuntu2 [4144 B] Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-python1.83.0 arm64 1.83.0-2.1ubuntu3 [307 kB] Get:215 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-bin arm64 1.15 [2336 B] Get:216 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi-python1.83.0 arm64 1.83.0-2.1ubuntu3 [353 kB] Get:217 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi-python1.83-dev arm64 1.83.0-2.1ubuntu3 [237 kB] Get:218 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-mpi-python-dev arm64 1.83.0.1ubuntu2 [4196 B] Get:219 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-2.1ubuntu3 [242 kB] Get:220 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-numpy1.83-dev arm64 1.83.0-2.1ubuntu3 [248 kB] Get:221 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-numpy-dev arm64 1.83.0.1ubuntu2 [4098 B] Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2.1ubuntu3 [317 kB] Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-program-options1.83-dev arm64 1.83.0-2.1ubuntu3 [391 kB] Get:224 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options-dev arm64 1.83.0.1ubuntu2 [4084 B] Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12t64 arm64 3.12.2-5ubuntu3 [2275 kB] Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libexpat1-dev arm64 2.6.1-2build1 [128 kB] Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-dev arm64 3.12.2-5ubuntu3 [5531 kB] Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3-dev arm64 3.12.2-0ubuntu2 [10.1 kB] Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12-dev arm64 3.12.2-5ubuntu3 [498 kB] Get:230 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:231 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-6 [149 kB] Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-dev arm64 3.12.2-0ubuntu2 [26.7 kB] Get:233 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-python1.83-dev arm64 1.83.0-2.1ubuntu3 [336 kB] Get:234 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-python-dev arm64 1.83.0.1ubuntu2 [4346 B] Get:235 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-random1.83.0 arm64 1.83.0-2.1ubuntu3 [242 kB] Get:236 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-random1.83-dev arm64 1.83.0-2.1ubuntu3 [242 kB] Get:237 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-random-dev arm64 1.83.0.1ubuntu2 [4062 B] Get:238 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-regex-dev arm64 1.83.0.1ubuntu2 [4324 B] Get:239 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-serialization-dev arm64 1.83.0.1ubuntu2 [4280 B] Get:240 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-stacktrace1.83.0 arm64 1.83.0-2.1ubuntu3 [288 kB] Get:241 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-stacktrace1.83-dev arm64 1.83.0-2.1ubuntu3 [246 kB] Get:242 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-stacktrace-dev arm64 1.83.0.1ubuntu2 [4066 B] Get:243 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-system-dev arm64 1.83.0.1ubuntu2 [4204 B] Get:244 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-test-dev arm64 1.83.0.1ubuntu2 [4090 B] Get:245 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-thread-dev arm64 1.83.0.1ubuntu2 [4088 B] Get:246 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-timer1.83.0 arm64 1.83.0-2.1ubuntu3 [241 kB] Get:247 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-timer1.83-dev arm64 1.83.0-2.1ubuntu3 [237 kB] Get:248 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-timer-dev arm64 1.83.0.1ubuntu2 [4190 B] Get:249 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-type-erasure1.83.0 arm64 1.83.0-2.1ubuntu3 [244 kB] Get:250 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-type-erasure1.83-dev arm64 1.83.0-2.1ubuntu3 [251 kB] Get:251 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-type-erasure-dev arm64 1.83.0.1ubuntu2 [4162 B] Get:252 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-url1.83.0 arm64 1.83.0-2.1ubuntu3 [342 kB] Get:253 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-url1.83-dev arm64 1.83.0-2.1ubuntu3 [451 kB] Get:254 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-url-dev arm64 1.83.0.1ubuntu2 [4190 B] Get:255 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-wave1.83.0 arm64 1.83.0-2.1ubuntu3 [448 kB] Get:256 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-wave1.83-dev arm64 1.83.0-2.1ubuntu3 [516 kB] Get:257 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-wave-dev arm64 1.83.0.1ubuntu2 [4096 B] Get:258 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-nowide1.83.0 arm64 1.83.0-2.1ubuntu3 [241 kB] Get:259 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-nowide1.83-dev arm64 1.83.0-2.1ubuntu3 [237 kB] Get:260 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-nowide-dev arm64 1.83.0.1ubuntu2 [4136 B] Get:261 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-all-dev arm64 1.83.0.1ubuntu2 [2286 B] Get:262 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcups2t64 arm64 2.4.7-1.2ubuntu3 [273 kB] Get:263 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] Get:264 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate-dev arm64 1.19-1 [51.2 kB] Get:265 http://ftpmaster.internal/ubuntu noble/universe arm64 libdouble-conversion3 arm64 3.3.0-1 [37.2 kB] Get:266 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] Get:267 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] Get:268 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] Get:269 http://ftpmaster.internal/ubuntu noble/main arm64 libwayland-server0 arm64 1.22.0-2.1 [34.0 kB] Get:270 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgbm1 arm64 24.0.3-1ubuntu4 [43.5 kB] Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglapi-mesa arm64 24.0.3-1ubuntu4 [58.3 kB] Get:273 http://ftpmaster.internal/ubuntu noble/main arm64 libwayland-client0 arm64 1.22.0-2.1 [25.6 kB] Get:274 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] Get:275 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] Get:276 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] Get:277 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] Get:278 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] Get:279 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] Get:280 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] Get:281 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libegl-mesa0 arm64 24.0.3-1ubuntu4 [116 kB] Get:282 http://ftpmaster.internal/ubuntu noble/main arm64 libegl1 arm64 1.7.0-1 [29.2 kB] Get:283 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] Get:284 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] Get:285 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] Get:286 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] Get:287 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] Get:288 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9build1 [5546 B] Get:289 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9build1 [27.0 kB] Get:290 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgl1-mesa-dri arm64 24.0.3-1ubuntu4 [8236 kB] Get:291 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglx-mesa0 arm64 24.0.3-1ubuntu4 [166 kB] Get:292 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] Get:293 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] Get:294 http://ftpmaster.internal/ubuntu noble/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:295 http://ftpmaster.internal/ubuntu noble/main arm64 x11proto-dev all 2023.2-1 [602 kB] Get:296 http://ftpmaster.internal/ubuntu noble/main arm64 libxau-dev arm64 1:1.0.9-1build5 [10.1 kB] Get:297 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp-dev arm64 1:1.1.3-0ubuntu5 [26.4 kB] Get:298 http://ftpmaster.internal/ubuntu noble/main arm64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:299 http://ftpmaster.internal/ubuntu noble/main arm64 libpthread-stubs0-dev arm64 0.4-1build2 [5496 B] Get:300 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1-dev arm64 1.15-1 [89.6 kB] Get:301 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-dev arm64 2:1.8.7-1 [738 kB] Get:302 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-dev arm64 1.7.0-1 [14.2 kB] Get:303 http://ftpmaster.internal/ubuntu noble/main arm64 libgl-dev arm64 1.7.0-1 [102 kB] Get:304 http://ftpmaster.internal/ubuntu noble/main arm64 libegl-dev arm64 1.7.0-1 [18.2 kB] Get:305 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu3 [384 kB] Get:306 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-long3 arm64 3.3.10-1ubuntu3 [640 kB] Get:307 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-single3 arm64 3.3.10-1ubuntu3 [583 kB] Get:308 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-bin arm64 3.3.10-1ubuntu3 [34.2 kB] Get:309 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfftw3-dev arm64 3.3.10-1ubuntu3 [1453 kB] Get:310 http://ftpmaster.internal/ubuntu noble/main arm64 libopengl0 arm64 1.7.0-1 [35.9 kB] Get:311 http://ftpmaster.internal/ubuntu noble/main arm64 libglu1-mesa arm64 9.0.2-1.1 [137 kB] Get:312 http://ftpmaster.internal/ubuntu noble/main arm64 libopengl-dev arm64 1.7.0-1 [3430 B] Get:313 http://ftpmaster.internal/ubuntu noble/main arm64 libglu1-mesa-dev arm64 9.0.2-1.1 [222 kB] Get:314 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] Get:315 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgudev-1.0-0 arm64 1:238-5ubuntu1 [15.1 kB] Get:316 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libharfbuzz0b arm64 8.3.0-2build2 [463 kB] Get:317 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] Get:318 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] Get:319 http://ftpmaster.internal/ubuntu noble/main arm64 libevdev2 arm64 1.13.1+dfsg-1 [35.1 kB] Get:320 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwacom-common all 2.10.0-2 [63.4 kB] Get:321 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwacom9 arm64 2.10.0-2 [23.7 kB] Get:322 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libinput-bin arm64 1.25.0-1ubuntu2 [22.2 kB] Get:323 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmtdev1t64 arm64 1.1.6-1.1build1 [14.3 kB] Get:324 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libinput10 arm64 1.25.0-1ubuntu2 [129 kB] Get:325 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] Get:326 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] Get:327 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] Get:328 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] Get:329 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] Get:330 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] Get:331 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] Get:332 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] Get:333 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] Get:334 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc-dev arm64 4.0.0+ds-4ubuntu1 [167 kB] Get:335 http://ftpmaster.internal/ubuntu noble/universe arm64 libmd4c0 arm64 0.4.8-1 [41.2 kB] Get:336 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmm8.0t64 arm64 8.0.0+dfsg-6.1ubuntu2 [948 kB] Get:337 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmm-dev arm64 8.0.0+dfsg-6.1ubuntu2 [327 kB] Get:338 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmm-plugins arm64 8.0.0+dfsg-6.1ubuntu2 [1126 kB] Get:339 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] Get:340 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] Get:341 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-5build1 [266 kB] Get:342 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] Get:343 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5core5t64 arm64 5.15.12+dfsg-3ubuntu7 [1972 kB] Get:344 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5concurrent5t64 arm64 5.15.12+dfsg-3ubuntu7 [35.8 kB] Get:345 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5dbus5t64 arm64 5.15.12+dfsg-3ubuntu7 [224 kB] Get:346 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5network5t64 arm64 5.15.12+dfsg-3ubuntu7 [740 kB] Get:347 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] Get:348 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-icccm4 arm64 0.4.1-1.1build2 [11.0 kB] Get:349 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-util1 arm64 0.4.0-1build2 [11.2 kB] Get:350 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-image0 arm64 0.4.0-2 [11.1 kB] Get:351 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-keysyms1 arm64 0.4.0-1build3 [8606 B] Get:352 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] Get:353 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render-util0 arm64 0.3.9-1build3 [10.2 kB] Get:354 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shape0 arm64 1.15-1 [6106 B] Get:355 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xinerama0 arm64 1.15-1 [5434 B] Get:356 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xinput0 arm64 1.15-1 [33.5 kB] Get:357 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xkb1 arm64 1.15-1 [31.7 kB] Get:358 http://ftpmaster.internal/ubuntu noble/main arm64 libxkbcommon0 arm64 1.6.0-1 [121 kB] Get:359 http://ftpmaster.internal/ubuntu noble/main arm64 libxkbcommon-x11-0 arm64 1.6.0-1 [13.6 kB] Get:360 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5gui5t64 arm64 5.15.12+dfsg-3ubuntu7 [3616 kB] Get:361 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5widgets5t64 arm64 5.15.12+dfsg-3ubuntu7 [2550 kB] Get:362 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5xml5t64 arm64 5.15.12+dfsg-3ubuntu7 [125 kB] Get:363 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5designer5 arm64 5.15.12-2build3 [2844 kB] Get:364 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5sql5t64 arm64 5.15.12+dfsg-3ubuntu7 [123 kB] Get:365 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5help5 arm64 5.15.12-2build3 [165 kB] Get:366 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5opengl5t64 arm64 5.15.12+dfsg-3ubuntu7 [148 kB] Get:367 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5printsupport5t64 arm64 5.15.12+dfsg-3ubuntu7 [210 kB] Get:368 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5test5t64 arm64 5.15.12+dfsg-3ubuntu7 [144 kB] Get:369 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan-dev arm64 1.3.275.0-1 [1239 kB] Get:370 http://ftpmaster.internal/ubuntu noble/main arm64 libxext-dev arm64 2:1.3.4-1build1 [85.5 kB] Get:371 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 qt5-qmake-bin arm64 5.15.12+dfsg-3ubuntu7 [1070 kB] Get:372 http://ftpmaster.internal/ubuntu noble/universe arm64 qtchooser arm64 66-2build1 [23.2 kB] Get:373 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 qt5-qmake arm64 5.15.12+dfsg-3ubuntu7 [209 kB] Get:374 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 qtbase5-dev-tools arm64 5.15.12+dfsg-3ubuntu7 [824 kB] Get:375 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 qtbase5-dev arm64 5.15.12+dfsg-3ubuntu7 [1124 kB] Get:376 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libqt5opengl5-dev arm64 5.15.12+dfsg-3ubuntu7 [42.3 kB] Get:377 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] Get:378 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsharpyuv0 arm64 1.3.2-0.4build3 [14.5 kB] Get:379 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsharpyuv-dev arm64 1.3.2-0.4build3 [15.1 kB] Get:380 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-dev arm64 3.45.1-1ubuntu2 [916 kB] Get:381 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] Get:382 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig-dev arm64 2.1-6.1ubuntu1 [27.3 kB] Get:383 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [178 kB] Get:384 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd-dev arm64 1.5.5+dfsg2-2 [343 kB] Get:385 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwebp7 arm64 1.3.2-0.4build3 [191 kB] Get:386 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwebpdemux2 arm64 1.3.2-0.4build3 [12.3 kB] Get:387 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwebpmux3 arm64 1.3.2-0.4build3 [25.0 kB] Get:388 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwebpdecoder3 arm64 1.3.2-0.4build3 [88.7 kB] Get:389 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libwebp-dev arm64 1.3.2-0.4build3 [334 kB] Get:390 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu2 [191 kB] Get:391 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtiffxx6 arm64 4.5.1+git230720-4ubuntu2 [5640 B] Get:392 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtiff-dev arm64 4.5.1+git230720-4ubuntu2 [337 kB] Get:393 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxslt1.1 arm64 1.1.39-0exp1build1 [166 kB] Get:394 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] Get:395 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] Get:396 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] Get:397 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] Get:398 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] Get:399 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-2 [48.6 kB] Get:400 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] Get:401 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-6ubuntu1 [3565 kB] Get:402 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-contourpy arm64 1.0.7-2build1 [163 kB] Get:403 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] Get:404 http://ftpmaster.internal/ubuntu noble/main arm64 python3-six all 1.16.0-4 [12.4 kB] Get:405 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] Get:406 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] Get:407 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] Get:408 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] Get:409 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] Get:410 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] Get:411 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tz all 2024.1-2 [31.4 kB] Get:412 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] Get:413 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-lxml arm64 5.1.0-1build2 [1254 kB] Get:414 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] Get:415 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] Get:416 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] Get:417 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] Get:418 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-kiwisolver arm64 1.4.4-2build1 [48.5 kB] Get:419 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libopenjp2-7 arm64 2.5.0-2build3 [171 kB] Get:420 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] Get:421 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-tk arm64 3.12.2-3ubuntu4 [102 kB] Get:422 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] Get:423 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pyparsing all 3.1.1-1 [86.2 kB] Get:424 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-packaging all 24.0-1 [41.1 kB] Get:425 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] Get:426 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pyqt5.sip arm64 12.13.0-1build3 [64.0 kB] Get:427 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pyqt5 arm64 5.15.10+dfsg-1build5 [2557 kB] Get:428 http://ftpmaster.internal/ubuntu noble/universe arm64 sip-dev arm64 4.19.25+dfsg-5build2 [178 kB] Get:429 http://ftpmaster.internal/ubuntu noble/universe arm64 libeigen3-dev all 3.4.0-4 [1056 kB] Get:430 http://ftpmaster.internal/ubuntu noble/universe arm64 voronota arm64 1.22.3149-2 [2000 kB] Preconfiguring packages ... Fetched 276 MB in 32s (8533 kB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15848 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-5ubuntu3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.2-5ubuntu3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.1-2build1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-5ubuntu3_arm64.deb ... Unpacking python3.12-minimal (3.12.2-5ubuntu3) ... Setting up libpython3.12-minimal:arm64 (3.12.2-5ubuntu3) ... Setting up libexpat1:arm64 (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-5ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 16166 files and directories currently installed.) 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Setting up libopenmm8.0t64 (8.0.0+dfsg-6.1ubuntu2) ... Setting up libwacom-common (2.10.0-2) ... Setting up libxkbcommon0:arm64 (1.6.0-1) ... Setting up libwayland-client0:arm64 (1.22.0-2.1) ... Setting up libjpeg8:arm64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2023.2-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:arm64 (2:1.0.10-1build2) ... Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libboost-wave1.83.0:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxcb1:arm64 (1.15-1) ... 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Setting up libboost-math-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libwebpdemux2:arm64 (1.3.2-0.4build3) ... Setting up python3.12 (3.12.2-5ubuntu3) ... Setting up libedit2:arm64 (3.1-20230828-1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ... Setting up libboost-system-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libpng-dev:arm64 (1.6.43-5build1) ... Setting up libxcb-keysyms1:arm64 (0.4.0-1build3) ... Setting up libxcb-shape0:arm64 (1.15-1) ... Setting up libavahi-common3:arm64 (0.8-13ubuntu5) ... Setting up libboost-serialization1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libjbig-dev:arm64 (2.1-6.1ubuntu1) ... Setting up libboost-locale1.83.0:arm64 (1.83.0-2.1ubuntu3) ... Setting up libboost-test1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up libboost-url1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxcb-render-util0:arm64 (0.3.9-1build3) ... Setting up libboost-tools-dev (1.83.0.1ubuntu2) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libboost-filesystem1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxcb-icccm4:arm64 (0.4.1-1.1build2) ... Setting up libboost-exception-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-nowide-dev (1.83.0.1ubuntu2) ... Setting up libopenmm-dev (8.0.0+dfsg-6.1ubuntu2) ... Setting up libxcb-util1:arm64 (0.4.0-1build2) ... Setting up pkgconf:arm64 (1.8.1-2) ... Setting up libinput-bin (1.25.0-1ubuntu2) ... Setting up libxcb-xkb1:arm64 (1.15-1) ... Setting up libxcb-image0:arm64 (0.4.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up libboost-test-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up libcifpp5:arm64 (5.0.7.1-3build1) ... Setting up libpython3.12t64:arm64 (3.12.2-5ubuntu3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-7) ... Setting up libxdmcp-dev:arm64 (1:1.1.3-0ubuntu5) ... Setting up libwebp-dev:arm64 (1.3.2-0.4build3) ... Setting up libxcb-xinerama0:arm64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libllvm17t64:arm64 (1:17.0.6-9build3) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up libboost-container1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up gfortran-13 (13.2.0-23ubuntu3) ... Setting up libboost-date-time1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libraqm0:arm64 (0.10.1-1) ... Setting up shared-mime-info (2.4-4) ... Setting up libboost-numpy-dev (1.83.0.1ubuntu2) ... Setting up libxkbcommon-x11-0:arm64 (1.6.0-1) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up icu-devtools (74.2-1ubuntu1) ... Setting up pkg-config:arm64 (1.8.1-2) ... Setting up libboost-random1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libboost-serialization-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-date-time-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-9ubuntu2) ... Setting up libopenmm-plugins (8.0.0+dfsg-6.1ubuntu2) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-3build2) ... Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu2) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libxslt1.1:arm64 (1.1.39-0exp1build1) ... Setting up libx11-6:arm64 (2:1.8.7-1) ... Setting up libboost-url-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libhwloc-dev:arm64 (2.10.0-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... Setting up libtiffxx6:arm64 (4.5.1+git230720-4ubuntu2) ... Setting up libsm6:arm64 (2:1.2.3-1build2) ... Setting up libarchive13t64:arm64 (3.7.2-2) ... Setting up libfftw3-dev:arm64 (3.3.10-1ubuntu3) ... Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... Setting up libavahi-client3:arm64 (0.8-13ubuntu5) ... Setting up libboost-timer-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-filesystem-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libpython3-stdlib:arm64 (3.12.2-0ubuntu2) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libboost-thread1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up libinput10:arm64 (1.25.0-1ubuntu2) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... Setting up libibverbs1:arm64 (50.0-2build2) ... Setting up fontconfig (2.15.0-1.1ubuntu2) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libboost-json1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxcb1-dev:arm64 (1.15-1) ... Setting up libboost-wave1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libboost-locale1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up libgbm1:arm64 (24.0.3-1ubuntu4) ... Setting up ibverbs-providers:arm64 (50.0-2build2) ... Setting up libdrm-radeon1:arm64 (2.4.120-2) ... Setting up openssh-client (1:9.6p1-3ubuntu12) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:arm64 (24.0.3-1ubuntu4) ... Setting up libboost-type-erasure1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... Setting up libx11-dev:arm64 (2:1.8.7-1) ... Setting up libxext6:arm64 (2:1.3.4-1build1) ... Setting up libboost-random-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-locale-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3 (3.12.2-0ubuntu2) ... Setting up libpython3.12-dev:arm64 (3.12.2-5ubuntu3) ... Setting up libboost-wave-dev:arm64 (1.83.0.1ubuntu2) ... Setting up dssp (4.2.2-2) ... Setting up man-db (2.12.0-4build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libboost-container-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-tz (2024.1-2) ... Setting up libboost-type-erasure-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... Setting up libboost-context1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... Setting up python3-six (1.16.0-4) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.3) ... Setting up libboost-coroutine1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up python3-pil:arm64 (10.2.0-1) ... Setting up libqt5core5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up python3-decorator (5.1.1-5) ... Setting up libegl-mesa0:arm64 (24.0.3-1ubuntu4) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up libtiff-dev:arm64 (4.5.1+git230720-4ubuntu2) ... Setting up libboost-fiber1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxfixes3:arm64 (1:6.0.0-2) ... Setting up python3-brotli (1.1.0-2build2) ... Setting up python3-cycler (0.11.0-2) ... Setting up libevent-dev (2.1.12-stable-9ubuntu2) ... Setting up python3-kiwisolver (1.4.4-2build1) ... Setting up python3.12-dev (3.12.2-5ubuntu3) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up libxext-dev:arm64 (2:1.3.4-1build1) ... Setting up python3-pyqt5.sip (12.13.0-1build3) ... Setting up python3-lxml:arm64 (5.1.0-1build2) ... Setting up libegl1:arm64 (1.7.0-1) ... Setting up libqt5sql5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up cmake (3.28.3-1build6) ... Setting up librdmacm1t64:arm64 (50.0-2build2) ... Setting up python3-dateutil (2.8.2-3) ... Setting up libboost-coroutine-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libxss1:arm64 (1:1.2.3-1build2) ... Setting up libboost-log1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-json-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-mpmath (1.2.1-3) ... Setting up libboost-regex-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libboost-log-dev (1.83.0.1ubuntu2) ... Setting up libcups2t64:arm64 (2.4.7-1.2ubuntu3) ... Setting up libhsakmt1:arm64 (5.7.0-1build1) ... Setting up libboost-thread-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-fiber-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libfabric1:arm64 (1.17.0-3build2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libvulkan-dev:arm64 (1.3.275.0-1) ... Setting up libqt5dbus5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libglx-mesa0:arm64 (24.0.3-1ubuntu4) ... Setting up libpython3-dev:arm64 (3.12.2-0ubuntu2) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up libglx0:arm64 (1.7.0-1) ... Setting up python3-lz4 (4.0.2+dfsg-1build4) ... Setting up libboost-iostreams1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up python3-unicodedata2 (15.1.0+ds-1) ... Setting up libqt5concurrent5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libtk8.6:arm64 (8.6.14-1build1) ... Setting up libqt5network5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libqt5xml5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libboost-context-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-iostreams-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libqt5test5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libibverbs-dev:arm64 (50.0-2build2) ... Setting up libhwloc-plugins:arm64 (2.10.0-1) ... Setting up libboost-graph1.83-dev:arm64 (1.83.0-2.1ubuntu3) ... Setting up python3-fs (2.4.16-3) ... Setting up qtbase5-dev-tools (5.15.12+dfsg-3ubuntu7) ... Setting up libgl1:arm64 (1.7.0-1) ... Setting up python3-dev (3.12.2-0ubuntu2) ... Setting up libboost-python1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libpmix2t64:arm64 (5.0.1-4.1build1) ... Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... Setting up libhsa-runtime64-1 (5.7.1-2build1) ... Setting up libglx-dev:arm64 (1.7.0-1) ... Setting up python3-contourpy (1.0.7-2build1) ... Setting up libgl-dev:arm64 (1.7.0-1) ... Setting up libpmix-dev:arm64 (5.0.1-4.1build1) ... Setting up dh-python (6.20240401) ... Setting up libboost-graph-dev:arm64 (1.83.0.1ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-scipy (1.11.4-6) ... Setting up libegl-dev:arm64 (1.7.0-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tk:arm64 (3.12.2-3ubuntu4) ... Setting up libboost-python-dev (1.83.0.1ubuntu2) ... Setting up libqt5gui5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libamdhip64-5 (5.2.3-12) ... Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... Setting up libglu1-mesa-dev:arm64 (9.0.2-1.1) ... Setting up libucx0:arm64 (1.16.0+ds-4build1) ... Setting up libqt5widgets5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libqt5help5:arm64 (5.15.12-2build3) ... Setting up libopenmpi3t64:arm64 (4.1.6-7ubuntu2) ... Setting up libqt5opengl5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libboost-mpi1.83.0 (1.83.0-2.1ubuntu3) ... Setting up openmpi-bin (4.1.6-7ubuntu2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libqt5printsupport5t64:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libboost-graph-parallel1.83.0 (1.83.0-2.1ubuntu3) ... Setting up libqt5designer5:arm64 (5.15.12-2build3) ... Setting up mpi-default-bin (1.15) ... Setting up qtbase5-dev:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libopenmpi-dev:arm64 (4.1.6-7ubuntu2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-2.1ubuntu3) ... Setting up python3-pyqt5 (5.15.10+dfsg-1build5) ... Setting up libboost-mpi-python1.83.0 (1.83.0-2.1ubuntu3) ... Setting up libqt5opengl5-dev:arm64 (5.15.12+dfsg-3ubuntu7) ... Setting up libboost-graph-parallel-dev (1.83.0.1ubuntu2) ... Setting up mpi-default-dev (1.15) ... Setting up libboost-mpi1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-dev (1.83.0.1ubuntu2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-2.1ubuntu3) ... Setting up libboost-mpi-python-dev (1.83.0.1ubuntu2) ... Setting up libboost-all-dev (1.83.0.1ubuntu2) ... Setting up python3-fonttools (4.46.0-1build2) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1ubuntu3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for systemd (255.4-1ubuntu6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 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libxcb-image0_0.4.0-2 libxcb-keysyms1_0.4.0-1build3 libxcb-present0_1.15-1 libxcb-randr0_1.15-1 libxcb-render-util0_0.3.9-1build3 libxcb-render0_1.15-1 libxcb-shape0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-util1_0.4.0-1build2 libxcb-xfixes0_1.15-1 libxcb-xinerama0_1.15-1 libxcb-xinput0_1.15-1 libxcb-xkb1_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 libxdmcp-dev_1:1.1.3-0ubuntu5 libxdmcp6_1:1.1.3-0ubuntu5 libxext-dev_2:1.3.4-1build1 libxext6_2:1.3.4-1build1 libxfixes3_1:6.0.0-2 libxft2_2.3.6-1 libxkbcommon-x11-0_1.6.0-1 libxkbcommon0_1.6.0-1 libxml2_2.9.14+dfsg-1.3ubuntu3 libxnvctrl0_510.47.03-0ubuntu4 libxrender1_1:0.9.10-1.1 libxshmfence1_1.3-1build4 libxslt1.1_1.1.39-0exp1build1 libxss1_1:1.2.3-1build2 libxxf86vm1_1:1.1.4-1build3 libxxhash0_0.8.2-2 libzstd-dev_1.5.5+dfsg2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-20.20 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2.4~exp1ubuntu3 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 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python3-dev_3.12.2-0ubuntu2 python3-fonttools_4.46.0-1build2 python3-fs_2.4.16-3 python3-kiwisolver_1.4.4-2build1 python3-lxml_5.1.0-1build2 python3-lz4_4.0.2+dfsg-1build4 python3-matplotlib_3.6.3-1ubuntu3 python3-minimal_3.12.2-0ubuntu2 python3-mpmath_1.2.1-3 python3-numpy_1:1.26.4+ds-6ubuntu1 python3-packaging_24.0-1 python3-pil_10.2.0-1 python3-pil.imagetk_10.2.0-1 python3-pkg-resources_68.1.2-2ubuntu1 python3-pyparsing_3.1.1-1 python3-pyqt5_5.15.10+dfsg-1build5 python3-pyqt5.sip_12.13.0-1build3 python3-scipy_1.11.4-6 python3-setuptools_68.1.2-2ubuntu1 python3-six_1.16.0-4 python3-sympy_1.12-7 python3-tk_3.12.2-3ubuntu4 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-unicodedata2_15.1.0+ds-1 python3.12_3.12.2-5ubuntu3 python3.12-dev_3.12.2-5ubuntu3 python3.12-minimal_3.12.2-5ubuntu3 qt5-qmake_5.15.12+dfsg-3ubuntu7 qt5-qmake-bin_5.15.12+dfsg-3ubuntu7 qtbase5-dev_5.15.12+dfsg-3ubuntu7 qtbase5-dev-tools_5.15.12+dfsg-3ubuntu7 qtchooser_66-2build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 shared-mime-info_2.4-4 sip-dev_4.19.25+dfsg-5build2 systemd_255.4-1ubuntu6 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu6 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tk8.6-blt2.5_2.5.3+dfsg-7 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 unicode-data_15.1.0-1 util-linux_2.39.3-9ubuntu4 uuid-runtime_2.39.3-9ubuntu4 voronota_1.22.3149-2 x11-common_1:7.7+23ubuntu2 x11proto-dev_2023.2-1 xkb-data_2.41-2 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: openstructure Binary: libost-base2.5, libost-bindings2.5, libost-conop2.5, libost-db2.5, libost-geom2.5, libost-gfx2.5, libost-gui2.5, libost-img-alg2.5, libost-img2.5, libost-info2.5, libost-io2.5, libost-mol-alg2.5, libost-mol-mm2.5, libost-mol2.5, libost-seq-alg2.5, libost-seq2.5, openstructure, python3-ost, libost-base-dev, libost-bindings-dev, libost-conop-dev, libost-db-dev, libost-geom-dev, libost-gfx-dev, libost-gui-dev, libost-img-alg-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-mm-dev, libost-mol-dev, libost-seq-alg-dev, libost-seq-dev Architecture: any Version: 2.5.0-1ubuntu1 Maintainer: Ubuntu Developers Uploaders: Andrius Merkys , Homepage: https://www.openstructure.org Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/debichem-team/openstructure Vcs-Git: https://salsa.debian.org/debichem-team/openstructure.git Testsuite: autopkgtest Testsuite-Triggers: clustalw, dssp, ncbi-blast+, voronota Build-Depends: clustalw , cmake, debhelper-compat (= 13), dh-python, dssp , libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev [amd64 arm64 ppc64el], libopenmm-plugins [amd64 arm64 ppc64el], libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib , python3-numpy , python3-pil , python3-pyqt5, python3-scipy , qtbase5-dev, sip-dev, voronota Package-List: libost-base-dev deb libdevel optional arch=any libost-base2.5 deb libs optional arch=any libost-bindings-dev deb libdevel optional arch=any libost-bindings2.5 deb libs optional arch=any libost-conop-dev deb libdevel optional arch=any libost-conop2.5 deb libs optional arch=any libost-db-dev deb libdevel optional arch=any libost-db2.5 deb libs optional arch=any libost-geom-dev deb libdevel optional arch=any libost-geom2.5 deb libs optional arch=any libost-gfx-dev deb libdevel optional arch=any libost-gfx2.5 deb libs optional arch=any libost-gui-dev deb libdevel optional arch=any libost-gui2.5 deb libs optional arch=any libost-img-alg-dev deb libdevel optional arch=any libost-img-alg2.5 deb libs optional arch=any libost-img-dev deb libdevel optional arch=any libost-img2.5 deb libs optional arch=any libost-info-dev deb libdevel optional arch=any libost-info2.5 deb libs optional arch=any libost-io-dev deb libdevel optional arch=any libost-io2.5 deb libs optional arch=any libost-mol-alg-dev deb libdevel optional arch=any libost-mol-alg2.5 deb libs optional arch=any libost-mol-dev deb libdevel optional arch=any libost-mol-mm-dev deb libdevel optional arch=amd64,arm64,ppc64el libost-mol-mm2.5 deb libs optional arch=amd64,arm64,ppc64el libost-mol2.5 deb libs optional arch=any libost-seq-alg-dev deb libdevel optional arch=any libost-seq-alg2.5 deb libs optional arch=any libost-seq-dev deb libdevel optional arch=any libost-seq2.5 deb libs optional arch=any openstructure deb science optional arch=any python3-ost deb python optional arch=any Checksums-Sha1: dc20545446d9a11067eb8eb0aa9e9a6bc27c00a0 26358304 openstructure_2.5.0.orig.tar.xz 39d784fe51d4e7907e72bda4ec33cdbb22fa45e4 92350396 openstructure_2.5.0-1ubuntu1.debian.tar.xz Checksums-Sha256: 2275f7dcd9b4fba2692ee7174cd33c0b31addd343a8c1fa183cebf84f7c131f9 26358304 openstructure_2.5.0.orig.tar.xz 6e596fd42fd774f2fbd793223a56e198649eebfea4010aa5e22597fa291407d3 92350396 openstructure_2.5.0-1ubuntu1.debian.tar.xz Files: 8a733fc70a8fe31871d0daf286aa0206 26358304 openstructure_2.5.0.orig.tar.xz 42fc9d5b970728a3850550bc62e58358 92350396 openstructure_2.5.0-1ubuntu1.debian.tar.xz Original-Maintainer: Debichem Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmWvl+AACgkQr8/sjmac 4cKx/Q/+IRNAabmdwzFGdrgVeXREahRSNHm+TAZOtnPSXbGvw6i/L+GgjtsYqXvN NAqTA8cLyoR5hASgWzfX8CTHdEvIPzr12nqNvUkSAXW+V7XD53mcr5ikc6hvO1Hk uwB7fSb7ifQFjIkDx73jjlxKWS3ZzK6/9ANubBmKOtan2ICGeR5f3tt+ZeG431wP ZlAfkl0nIoG33EWApnCBgz9ChmRj2PvgAJgenQAVlR8HrU6HlHE79XauDxnVWGo9 fPks01s1a5nK0w1lxIrvT0S9kpsV4Qem3H5wxtNYWgKky0f3hQDv0cjivSaCDRsB 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dpkg-source: info: applying fix-quotes-in-ENV.patch dpkg-source: info: applying skip-network-tests.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying ost_config.patch dpkg-source: info: applying skip-dssp-tests.patch dpkg-source: info: applying add-dummy-test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27674365 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27674365 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27674365 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.5.0-1ubuntu1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/aarch64-linux-gnu/openmm/plugins cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/aarch64-linux-gnu/openmm/plugins .. -- The CXX compiler identification is GNU 13.2.0 -- The C compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done CMake Warning (dev) at cmake_support/OST.cmake:892 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/OST.cmake:921 (get_compiler_version) CMakeLists.txt:174 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.12.2", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python312 -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: unit_test_framework -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: filesystem system -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: iostreams -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: program_options -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: regex -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: thread -- Found OpenGL: /usr/lib/aarch64-linux-gnu/libOpenGL.so -- Found EIGEN: /usr/include/eigen3 (Required is at least version "3.2.0") -- Found SQLITE3: /usr/lib/aarch64-linux-gnu/libsqlite3.so (Required is at least version "3.7.13") -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3") -- Found PNG: /usr/lib/aarch64-linux-gnu/libpng.so (found version "1.6.43") -- Found FFTW: /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/aarch64-linux-gnu/libtiff.so (found version "4.5.1") -- Found OpenMM: /usr/lib/aarch64-linux-gnu/libOpenMM.so -- Searching for python module PyQt5 for /usr/bin/python3 -- Found python module PyQt5 -- Searching for python module PyQt5.sip for /usr/bin/python3 -- Found python module PyQt5.sip -- OpenStructure will be built with the following options: Install Prefix (-DPREFIX) : /usr RPath in install (-DUSE_RPATH) : OFF Info support (-DENABLE_INFO) : ON Graphical interface (-DENABLE_GUI) : ON OpenGL support (-DENABLE_GFX) : ON Shader support (-DUSE_SHADER) : OFF Numpy support (-DUSE_NUMPY) : OFF SpaceNav Device support (-DENABLE_SPNAV) : OFF OpenMM support (-DENABLE_MM) : ON OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : /usr/lib/aarch64-linux-gnu/openmm/plugins Optimize (-DOPTIMIZE) : ON Profiling support (-DPROFILE) : OFF Double Precision (-DUSE_DOUBLE_PRECISION) : OFF Compound Lib (-DCOMPOUND_LIB) : NONE TMAlign and TMScore (-DCOMPILE_TMTOOLS) : OFF Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF -- Configuring done (3.7s) -- Generating done (1.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<>/obj-aarch64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a cd obj-aarch64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles /<>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/pymod /<>/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/pymod /<>/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/pymod /<>/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/<>/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /<>/cmake_support/substitute.cmake make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/lib make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./__init__.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/conop/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/bin make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./lga.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./lga.py cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/conop/pymod/./cleanup.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./cleanup.py cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/tests cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./hbplus.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hbplus.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target subst___init__.py make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/pymod /<>/obj-aarch64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./msms.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./msms.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_conop_pymod make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/pymod /<>/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./tmtools.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./tmtools.py make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/db/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/db/./__init__.py [ 0%] Built target create_stage make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./dssp.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dssp.py make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/pymod /<>/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/geom/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/geom/./__init__.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./clustalw.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./clustalw.py make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./__init__.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_db_pymod make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./utils.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./utils.py cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/pymod/./py_gfx_obj.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./py_gfx_obj.py [ 0%] Built target ost_geom_pymod make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/src /<>/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/share /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/share /<>/obj-aarch64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./naccess.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./naccess.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./hhblits.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build [ 0%] Built target ost_gfx_pymod make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/add_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_option_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./hhblits2.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits2.py make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/share /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/share /<>/obj-aarch64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/close_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./hhblits3.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits3.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/images/logo-small.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/critical_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./blast.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./blast.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/selection_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/delete_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./cadscore.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./cadscore.py [ 0%] Built target gui_images make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/measure_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/pymod /<>/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/distance_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./kclust.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./kclust.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_option.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/find_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./ialign.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./ialign.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/information_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./mmseqs2.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./mmseqs2.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/color_options_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_options_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/map_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/pymod/./dockq.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dockq.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/color_select_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_select_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/menubar_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/manipulator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/combo_options_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/combo_options_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/rigid_body_manipulator_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/cpk_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/cpk_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/selection_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png [ 0%] Built target ost_bindings_pymod make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/custom_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/custom_widget.py make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/pymod /<>/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/mouse_event.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/gradient_editor_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_editor_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/show_sidebar_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/dng/__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/gradient_info_handler.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_info_handler.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/map_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/dng/termuse.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/termuse.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/site_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/gradient_list_model.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_list_model.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/dng/superpositiondialog.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/superpositiondialog.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/align_properties_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/split_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/gradient_preset_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_preset_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/base_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/dng/init.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/init.py cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/warning_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/hsc_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/hsc_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/background_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /<>/modules/gui/share/icons/refresh.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/dng/menu.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/menu.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/immutable_gradient_info_handler.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/conservation_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/immutable_preset_info_handler.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_preset_info_handler.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target scene_icons make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/pymod /<>/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/init_inspector.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/init_inspector.py [ 0%] Built target ost_gui_dng_pymod make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/secstr_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/pymod /<>/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/inspector_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/inspector_widget.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./init_context_menu.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_context_menu.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/map_level_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/map_level_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_selection_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./init_menubar.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_menubar.py [ 0%] Built target ost_img_pymod make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_text_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset.py make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_delegate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./init_spacenav.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_spacenav.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/alg/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/remote.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/remote.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./init_splash.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_splash.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset_editor_list_model.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_list_model.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./trajectory_viewer.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./trajectory_viewer.py [ 0%] Built target ost_img_alg_pymod cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset_editor_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_widget.py make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/pymod /<>/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./helpwidget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./helpwidget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_search_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./table.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./table.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset_info_handler.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_info_handler.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_table_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/info/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/info/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset_list_model.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_list_model.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/./gosty_startup.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./gosty_startup.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/preset_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/tick_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_info_pymod make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/render_mode_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_mode_widget.py [ 0%] Built target ost_gui_pymod make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/pymod /<>/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake "--color=" make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/title_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/render_op.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_op.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/render_options_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_options_widget.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/alignment_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/io/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/scene_observer_impl.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_observer_impl.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/io/pymod/./remote.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./remote.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/base_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh [ 0%] Built target ost_mol_pymod make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/scene_selection_helper.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_selection_helper.py make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/io/pymod/./repository.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./repository.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/simple_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/simple_widget.py make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./__init__.py [ 0%] Built target ost_io_pymod cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/main_thread_runner.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/src /<>/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/sline_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/sline_widget.py cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./views.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./views.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/output_redirector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./superpose.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./superpose.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/toolbar_options_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/toolbar_options_widget.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./forcefield.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/completer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/trace_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/trace_widget.py cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./qsscoring.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscoring.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./ff_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/dir_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/tube_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/tube_widget.py cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./trajectory_analysis.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./buildingblock.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/gutter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./structure_analysis.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./structure_analysis.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/uniform_color_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/uniform_color_widget.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/path_completer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/visibility_op.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/visibility_op.py cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./helix_kinks.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./helix_kinks.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_context_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/line_trace_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/line_trace_widget.py cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./hbond.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./hbond.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./gromacs_block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_completer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./lddt.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./lddt.py cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/wireframe_widget.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/wireframe_widget.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./heuristic_block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/query_editor.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/query_editor.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./interaction.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./qsscore.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscore.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./settings.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./settings.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./scoring.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./scoring.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh [ 0%] Built target ost_gui_scene_pymod make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./simulation.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./chain_mapping.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./chain_mapping.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_tokenizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./modeller.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_syntax_highlighter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./stereochemistry.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./stereochemistry.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/pymod/./antechamber.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./antechamber.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/text_logger.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./ligand_scoring.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.py cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./state_extractor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/./dockq.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./dockq.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_interpreter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./system_creator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh [ 0%] Built target ost_mol_mm_pymod make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_interpreter_worker.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./topology_creator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/pymod/stereo_data.json /<>/obj-aarch64-linux-gnu/stage/share/openstructure/stereo_data.json cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./index.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./index.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_text_document_layout.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/./__init__.py [ 0%] Built target ost_mol_alg_pymod cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./topology.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology.hh make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/shell_history.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./steep.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./steep.hh make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/./__init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./__init__.py [ 0%] Built target ost_seq_pymod cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/state_machine.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/./mat.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./mat.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/./renumber.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./renumber.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/transition.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh [ 0%] Built target ost_mol_mm_headers make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/./aaindex.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./aaindex.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/transition_guard.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh [ 0%] Built target subst_ost_startup.py make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/aaindex1 /<>/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/button_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/aaindex2 /<>/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/drop_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/pymod/aaindex3 /<>/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 [ 0%] Built target subst_ost_config make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake [ 0%] Built target subst_ost [ 0%] Built target ost_seq_alg_pymod make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/bottom_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/actions /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/actions /<>/obj-aarch64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/src /<>/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/button_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_box.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /<>/actions/ost-compare-ligand-structures /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build [ 0%] Built target subst_dng make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/export_helper/vector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/event_button.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/event_button.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/config /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/config /<>/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /<>/actions/ost-compare-structures /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_widget_container.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./def.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./exc.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./exc.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_bar_widget_holder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /<>/obj-aarch64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /<>/actions/ost-compare-structures-legacy /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures-legacy make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./base.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/side_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./geom.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./geom.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./config.hh [ 0%] Built target actions cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/splitter_panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./dllexport.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./dllexport.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/tabbed_panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/generic_property_def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./version.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./version.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat3.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/context_menu.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/pair_to_tuple_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/current_selection_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat4.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/vec_to_list_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh [ 0%] Built target ost_config_headers make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/custom_part_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/pymod /<>/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/test_utils/compare_files.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/entity_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec2.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./generic_property.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./generic_property.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/entity_part_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./settings.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./settings.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/gfx_scene_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./integrity_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./integrity_error.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./stutil.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/label_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./invalid_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec4.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./table.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/root_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./ptr_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat2_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./log.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./log.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/render_mode_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./table_selector.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table_selector.py cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./log_sink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./log_sink.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/render_modes_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./xmlrunner.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./xmlrunner.py cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat3_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat4_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./profile.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/base/pymod/./testutils.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./testutils.py cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./circular_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./dyn_cast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/__init__.py cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_win_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./stdint.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./stdint.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./constants.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./constants.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite.hh [ 0%] Built target ost_base_pymod make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/message_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/src /<>/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./stdint_msc.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/message_box_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/log_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./range.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./range.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/argand.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./units.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./units.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite2_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./message.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./message.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite3_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./aligned_cuboid.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./platform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./platform.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec_mat_predicates.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./string_ref.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./string_ref.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/draw_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/drawing_functions.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./quat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./quat.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./pod_vector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./pod_vector.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./fixed_string.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./fixed_string.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./alignment_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/fft_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./tri_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./point_cloud.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/info_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./boost_filesystem_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/img2qt.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./paged_array.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./paged_array.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_region.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/mask_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/null_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_column.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column.hh [ 0%] Built target ost_geom_headers [ 0%] Built target ost_base_headers make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/src /<>/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/src /<>/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_column_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/pointer_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./invalid_sequence.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_error.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./views_from_sequences.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./profile_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_gui.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/chain_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_group.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/chain_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/pointlist_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh [ 0%] Built target ost_seq_headers cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/connector_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_item.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_item.hh make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/src /<>/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/pointlist_overlay_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/connector_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/strategies.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/src/./wrap_tmalign.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/dihedral.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/strategies_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/entity_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_path.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_path.hh [ 0%] Built target ost_bindings_headers make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/src /<>/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_set.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_set.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/viewer_normalizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/entity_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_visitor.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./conop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./conop.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_browser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/fragment_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_verbose_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./processor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./processor.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_type_dialog.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./item_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/fragment_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./amino_acids.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./diag.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./diag.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_ast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gl_canvas.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./geom_info_conversion.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./model_check.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_ast_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gl_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./item_type_cast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./scene_menu.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./heuristic.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./heuristic.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gosty_app.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh [ 0%] Built target ost_info_headers make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/src /<>/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound_lib.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/residue_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./sqlite_wrap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./admin.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./admin.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/residue_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./sqlite_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./rule_based.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/surface_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./minimal_compound_lib.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/surface_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main_area.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound_lib_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./linear_indexer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/torsion_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./perspective.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./ring_finder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./binary_container.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/torsion_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./extract_data_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./scene_selection.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_base.hh [ 0%] Built target ost_conop_headers make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/src /<>/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main_window.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_handle.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build [ 0%] Built target ost_db_headers cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_view.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./alignment_opts.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/src /<>/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./dock_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bond_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./clip_alignment.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./dock_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/raster_image/raster_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bond_table.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/dispatch.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./thin_splitter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./conservation.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./contact_prediction_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./contact_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_geom_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./distance_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_pool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./entropy.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_registry.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_state_saver.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./global_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_loader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_loader.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./ins_del.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_frequency_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chem_class.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_class.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./local_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh [ 0%] Built target ost_gui_headers cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chem_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_type.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/src /<>/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./merge_pairwise_alignments.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_spatial_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./anisotropic.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./pair_subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./auto_correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./in_mem_coord_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./semiglobal_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./clear.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_frame.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./sequence_identity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./editor_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_visitor_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./clip_min_max.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./sequence_similarity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./editor_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/index.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./conjugate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./mol.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./mol.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./convolute.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./variance_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/value_holder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./circle_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./cross_correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./composite_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./density_slice.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./hmm_pseudo_counts.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./dft.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./hmm_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_observer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fft.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fft.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_property_mapper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fftw_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_types.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_types.hh [ 0%] Built target ost_seq_alg_headers make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/src /<>/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fill.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_view.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/chemdict_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./filter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./debug.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./debug.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fourier_filters.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/star_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian_gradient_magnitude.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./dllexport.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./dllexport.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_visitor_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./handle_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./ics_editor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/io_profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian_laplacian.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/dcd_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./not_connected_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./property_id.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./highest_peak_search_3d.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_crd_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./histogram.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_pqr_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./line_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_handle_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_mae_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./local_sigma_threshold.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./mask_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_mmcif_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./negate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_list.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./normalizer_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_state_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_pdb_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./sec_structure.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./normalizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_linear.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./spatial_organizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_sdf_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_log.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./inverted_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_od.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_builder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./map.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./power_spectrum.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./builder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./builder.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./randomize.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/save_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./smooth_mask_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/load_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./torsion_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/surface_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat_accumulator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./transfer_connectivity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/load_surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_view_wrapper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat_min_max.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/surface_io_msms_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./threshold.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./normalizer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transcendentals.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./normalizer_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./null_data.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./null_data.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transform_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./xcs_editor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/stereochemical_params_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./observable.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./observable.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bounding_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/omf.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_mirror.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./paste_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/load_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_shift.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./peak.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./peak.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_df3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./discrete_shrink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./phase.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./phase.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/image_format.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transformation_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh [ 0%] Built target ost_mol_headers make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./physical_units.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./physical_units.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/src /<>/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dx_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./pixel_sampling.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transformations.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformations.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_spi_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./svd_superpose.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./point_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./point_list.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fractional_shift.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_situs_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./point.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./point.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./sec_structure_segments.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./polygon_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_mrc_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./polar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./local_dist_diff_test.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./progress.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./progress.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dat_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./size.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./size.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_ipl_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./line_average.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./distance_test_common.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./distance_rmsd_test.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_jpk_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./rscrosscorr.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./spherical_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./util.cc /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./util.cc cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./superpose_frames.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_nanoscope_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./util.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./filter_clashes.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh [ 0%] Built target ost_img_alg_headers make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/src /<>/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./value_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./value_util.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_png_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./construct_cbeta.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./vecmat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./vecmat.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./clash_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_info_convert.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dm3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./trajectory_analysis.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_tiff_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen_s.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./structure_analysis.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh [ 0%] Built target ost_img_headers make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/config /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/config /<>/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/tiff_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen_s.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./consistency_checks.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/jpk_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/jpk_util.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_spec.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./pdbize.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/sequence_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_octree.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh [ 0%] Built target ost_config make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/src /<>/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./adjacency_bitmap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/fasta_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/octree_isocont.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./consistency_checks.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/pir_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./contact_overlap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/promod_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/cartoon_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /<>/modules/geom/src/mat2.cc cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/custom_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./domain_find.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/profile_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/hhm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/cpk_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./similarity_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/pssm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/debug_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./accessibility.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/clustal_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/simple_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./sec_struct.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/load.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/sline_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./nonstandard.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/save.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/save.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./molck.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/trace_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./binary_data_sink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./find_membrane.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/line_trace_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./entity_to_density.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/backbone_trace.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./binary_data_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_source.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_detail.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh [ 0%] Built target ost_mol_alg_headers cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./container_serialization.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/trace_renderer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -MF CMakeFiles/ost_geom.dir/mat3.cc.o.d -o CMakeFiles/ost_geom.dir/mat3.cc.o -c /<>/modules/geom/src/mat3.cc cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./swap_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/connect_renderer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_utils.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/mapped_property.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_exception.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_renderer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./convert.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./convert.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/tabulated_trig.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./converting_streams.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./formatted_line.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/fast_spheres.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/chemdict_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/line_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/star_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/custom_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/cpk_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/simple_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/io_profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/sline_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/dcd_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_crd_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/line_trace_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/cartoon_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_pqr_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/trace_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_mae_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_mmcif_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/by_element_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/by_chain_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/uniform_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_pdb_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/gradient_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/entity_view_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_sdf_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/basic_gradient_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/gradient_level_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/map_handle_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/save_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./render_pass.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./bitmap_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/load_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/surface_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./collada_exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./color.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./color.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/load_surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/surface_io_msms_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./entity_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gl_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_str.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_str.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/stereochemical_params_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/omf.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./omf.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/sequence_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/fasta_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/pir_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/promod_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/profile_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_prim.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/hhm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./symmetry_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/pssm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_test_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/clustal_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./glwin_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/load.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./input.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./input.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./prim_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/save.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./save.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/load_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_map.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./scene.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_df3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./selection.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/image_format.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./image_format.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dx_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./texture.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_spi_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./vertex_array.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_situs_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./vertex_array_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./scene_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gl_include.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_mrc_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./glext_include.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dat_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_ipl_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./render_mode.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./material.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./material.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_jpk_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_nanoscope_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gradient.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_png_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gradient_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dm3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./primitives.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_tiff_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./povray_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/tiff_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./povray.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/jpk_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_io_headers cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./exporter_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -MF CMakeFiles/ost_geom.dir/mat4.cc.o.d -o CMakeFiles/ost_geom.dir/mat4.cc.o -c /<>/modules/geom/src/mat4.cc cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gost_exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./color_ops/map_handle_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_iso.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_slab.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_iso_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_gfx_headers [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -MF CMakeFiles/ost_geom.dir/vec3.cc.o.d -o CMakeFiles/ost_geom.dir/vec3.cc.o -c /<>/modules/geom/src/vec3.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /<>/modules/geom/src/vecmat2_op.cc [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat3_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -c /<>/modules/geom/src/vecmat3_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /<>/modules/geom/src/vecmat4_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -MF CMakeFiles/ost_geom.dir/composite2.cc.o.d -o CMakeFiles/ost_geom.dir/composite2.cc.o -c /<>/modules/geom/src/composite2.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /<>/modules/geom/src/composite3.cc In file included from /<>/modules/geom/src/composite2.hh:27, from /<>/modules/geom/src/composite2.cc:23: /<>/modules/geom/src/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/geom/src/def.hh:26, from /<>/modules/geom/src/composite2.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/geom/src/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /<>/modules/geom/src/composite2_op.cc /<>/modules/geom/src/composite3.cc: In member function ‘geom::Quat geom::Rotation3::GetQuat() const’: /<>/modules/geom/src/composite3.cc:218:27: note: parameter passing for argument of type ‘geom::Quat’ when C++17 is enabled changed to match C++14 in GCC 10.1 218 | Quat Rotation3::GetQuat() const | ^~~~~ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /<>/modules/geom/src/composite3_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -MF CMakeFiles/ost_geom.dir/quat.cc.o.d -o CMakeFiles/ost_geom.dir/quat.cc.o -c /<>/modules/geom/src/quat.cc In file included from /<>/modules/geom/src/composite2.hh:27, from /<>/modules/geom/src/composite2_op.hh:24, from /<>/modules/geom/src/composite2_op.cc:24: /<>/modules/geom/src/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/geom/src/composite2_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/geom/src/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /<>/modules/geom/src/transform.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /<>/modules/geom/src/aligned_cuboid.cc /<>/modules/geom/src/quat.cc: In function ‘geom::Quat geom::{anonymous}::extract_from_rotmat(const geom::Mat3&)’: /<>/modules/geom/src/quat.cc:185:41: note: parameter passing for argument of type ‘geom::Quat’ when C++17 is enabled changed to match C++14 in GCC 10.1 185 | Quat extract_from_rotmat(const Mat3& rot) | ^ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /<>/modules/geom/src/point_cloud.cc [ 1%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_geom.so.2.5 -o ../../../stage/lib/libost_geom.so.2.5.0 CMakeFiles/ost_geom.dir/mat2.cc.o CMakeFiles/ost_geom.dir/mat3.cc.o CMakeFiles/ost_geom.dir/mat4.cc.o CMakeFiles/ost_geom.dir/vec3.cc.o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o CMakeFiles/ost_geom.dir/composite2.cc.o CMakeFiles/ost_geom.dir/composite3.cc.o CMakeFiles/ost_geom.dir/composite2_op.cc.o CMakeFiles/ost_geom.dir/composite3_op.cc.o CMakeFiles/ost_geom.dir/quat.cc.o CMakeFiles/ost_geom.dir/transform.cc.o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o CMakeFiles/ost_geom.dir/point_cloud.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_geom.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5 ../../../stage/lib/libost_geom.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 1%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/pymod /<>/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -MF CMakeFiles/ost_base.dir/generic_property.cc.o.d -o CMakeFiles/ost_base.dir/generic_property.cc.o -c /<>/modules/base/src/generic_property.cc cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /<>/modules/geom/pymod/export_vec2.cc cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /<>/modules/geom/pymod/export_vecmat2_op.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /<>/modules/base/src/log.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /<>/modules/base/src/log_sink.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /<>/modules/base/src/profile.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /<>/modules/base/src/units.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /<>/modules/base/src/string_ref.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /<>/modules/base/src/platform.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vec2.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vec2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vecmat2_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /<>/modules/base/src/message.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /<>/modules/base/src/test_utils/compare_files.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /<>/modules/geom/pymod/export_vec3.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /<>/modules/geom/pymod/export_vecmat3_op.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /<>/modules/base/src/boost_filesystem_helper.cc [ 3%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_base.so.2.5 -o ../../../stage/lib/libost_base.so.2.5.0 CMakeFiles/ost_base.dir/generic_property.cc.o CMakeFiles/ost_base.dir/log.cc.o CMakeFiles/ost_base.dir/log_sink.cc.o CMakeFiles/ost_base.dir/profile.cc.o CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_base.so.2.5 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 3%] Built target ost_base make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/src /<>/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 3%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o -MF CMakeFiles/ost_info.dir/info_impl.cc.o.d -o CMakeFiles/ost_info.dir/info_impl.cc.o -c /<>/modules/info/src/info_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_impl.hh:41, from /<>/modules/info/src/info_impl.cc:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/info/src/info_impl.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vecmat3_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vec3.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vec3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec4.cc.o -c /<>/modules/geom/pymod/export_vec4.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /<>/modules/geom/pymod/export_vecmat4_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vec4.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vec4.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_vecmat4_op.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /<>/modules/geom/pymod/wrap_geom.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /<>/modules/geom/pymod/export_mat2.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /<>/modules/geom/pymod/export_mat3.cc [ 3%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /<>/modules/info/src/info_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/wrap_geom.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/wrap_geom.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_mat2.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_mat2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat4.cc.o -c /<>/modules/geom/pymod/export_mat4.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_group.hh:33, from /<>/modules/info/src/info.hh:32, from /<>/modules/info/src/info_handle.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/info/src/info_handle.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_mat3.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_mat3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2.cc.o -c /<>/modules/geom/pymod/export_composite2.cc [ 3%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /<>/modules/info/src/info_group.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_group.hh:33, from /<>/modules/info/src/info.hh:32, from /<>/modules/info/src/info_group.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/info/src/info_handle.hh:31, from /<>/modules/info/src/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /<>/modules/geom/pymod/export_composite3.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_mat4.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_mat4.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_composite2.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_composite2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /<>/modules/info/src/info_item.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_composite3.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_composite3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_group.hh:33, from /<>/modules/info/src/info.hh:32, from /<>/modules/info/src/info_item.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/info/src/info_item.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/preprocessor/iteration/detail/iter/limits/forward1_256.hpp:14, from /usr/include/boost/preprocessor/iteration/detail/iter/forward1.hpp:1343, from /usr/include/boost/python/detail/invoke.hpp:61, from /usr/include/boost/python/detail/caller.hpp:16, from /usr/include/boost/python/object/function_handle.hpp:8, from /usr/include/boost/python/converter/arg_to_python.hpp:19, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22: /usr/include/boost/python/detail/invoke.hpp: In function ‘PyObject* boost::python::detail::invoke(invoke_tag_, const RC&, F&, TC&) [with RC = boost::python::to_python_value; F = geom::Quat (geom::Rotation3::*)() const; TC = boost::python::arg_from_python]’: /usr/include/boost/python/detail/invoke.hpp:86:25: note: parameter passing for argument of type ‘geom::Quat’ when C++17 is enabled changed to match C++14 in GCC 10.1 86 | return rc( (tc().*f)(BOOST_PP_ENUM_BINARY_PARAMS_Z(1, N, ac, () BOOST_PP_INTERCEPT)) ); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /<>/modules/info/src/info_path.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /<>/modules/geom/pymod/export_composite2_op.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /<>/modules/info/src/info_set.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /<>/modules/geom/pymod/export_composite3_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_group.hh:33, from /<>/modules/info/src/info_set.hh:29, from /<>/modules/info/src/info_set.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/info/src/info_set.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_composite2_op.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_composite2_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /<>/modules/geom/pymod/export_quat.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_composite3_op.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_composite3_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /<>/modules/geom/pymod/export_transform.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/pymod/export_quat.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/geom/pymod/export_quat.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/geom/pymod/export_quat.cc: In function ‘geom::Quat normalize(const geom::Quat&)’: /<>/modules/geom/pymod/export_quat.cc:24:42: note: parameter passing for argument of type ‘geom::Quat’ when C++17 is enabled changed to match C++14 in GCC 10.1 24 | geom::Quat normalize (const geom::Quat& q) | ^ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /<>/modules/info/src/info_visitor.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /<>/modules/info/src/geom_info_conversion.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/info/src/geom_info_conversion.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /<>/modules/info/src/info_verbose_visitor.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/info/src/info_group.hh:33, from /<>/modules/info/src/info_verbose_visitor.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/info/src/info_verbose_visitor.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/geom/_ost_geom.so cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 [ 6%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.5 -o ../../../stage/lib/libost_info.so.2.5.0 CMakeFiles/ost_info.dir/info_impl.cc.o CMakeFiles/ost_info.dir/info_handle.cc.o CMakeFiles/ost_info.dir/info_group.cc.o CMakeFiles/ost_info.dir/info_item.cc.o CMakeFiles/ost_info.dir/info_path.cc.o CMakeFiles/ost_info.dir/info_set.cc.o CMakeFiles/ost_info.dir/info_visitor.cc.o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_info.so.2.5 ../../../stage/lib/libost_info.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 6%] Built target ost_info make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/src /<>/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/src /<>/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build cd /<>/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/geom/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -MF CMakeFiles/ost_img.dir/composite_mask.cc.o.d -o CMakeFiles/ost_img.dir/composite_mask.cc.o -c /<>/modules/img/base/src/composite_mask.cc cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /<>/modules/mol/base/src/atom_base.cc [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /<>/modules/img/base/src/circle_mask.cc make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 6%] Built target _ost_geom [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /<>/modules/mol/base/src/atom_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/circle_mask.hh:25, from /<>/modules/img/base/src/circle_mask.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/mask_base.hh:27, from /<>/modules/img/base/src/composite_mask.hh:28, from /<>/modules/img/base/src/composite_mask.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, from /<>/modules/mol/base/src/atom_base.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/modules/mol/base/src/atom_base.hh:22, from /<>/modules/mol/base/src/atom_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /<>/modules/mol/base/src/atom_handle.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/atom_handle.hh:22, from /<>/modules/mol/base/src/atom_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /<>/modules/img/base/src/data_algorithm.cc [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /<>/modules/img/base/src/data_observer.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /<>/modules/mol/base/src/atom_view.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF CMakeFiles/ost_img.dir/data.cc.o.d -o CMakeFiles/ost_img.dir/data.cc.o -c /<>/modules/img/base/src/data.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /<>/modules/mol/base/src/bond_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/data.hh:36, from /<>/modules/img/base/src/image_handle.hh:38, from /<>/modules/img/base/src/data_observer.hh:31, from /<>/modules/img/base/src/data_observer.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/base/src/data_observer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -MF CMakeFiles/ost_img.dir/extent_iterator.cc.o.d -o CMakeFiles/ost_img.dir/extent_iterator.cc.o -c /<>/modules/img/base/src/extent_iterator.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/data.hh:36, from /<>/modules/img/base/src/data.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/data.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/mol/base/src/residue_view.hh:22, from /<>/modules/mol/base/src/atom_view.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/atom_view.hh:25, from /<>/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /<>/modules/mol/base/src/bond_handle.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/list:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, from /<>/modules/mol/base/src/bond_handle.hh:22, from /<>/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /<>/modules/img/base/src/extent_mask.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /<>/modules/mol/base/src/chain_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/extent_iterator.hh:30, from /<>/modules/img/base/src/extent_iterator.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/img/base/src/point.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /<>/modules/img/base/src/extent.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/extent.hh:34, from /<>/modules/img/base/src/extent_mask.hh:28, from /<>/modules/img/base/src/extent_mask.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /<>/modules/img/base/src/image_factory.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, from /<>/modules/mol/base/src/chain_base.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/chain_base.hh:22, from /<>/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/extent.hh:34, from /<>/modules/img/base/src/extent.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/base/src/extent.cc:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /<>/modules/mol/base/src/chain_handle.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /<>/modules/mol/base/src/chain_view.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /<>/modules/img/base/src/image_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/extent.hh:34, from /<>/modules/img/base/src/image_factory.hh:32, from /<>/modules/img/base/src/image_factory.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/image_factory.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/chain_handle.hh:26, from /<>/modules/mol/base/src/chain_handle.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/chain_handle.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /<>/modules/img/base/src/image_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/mol/base/src/chain_view.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/data.hh:36, from /<>/modules/img/base/src/image_handle.hh:38, from /<>/modules/img/base/src/image_handle.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/image_handle.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /<>/modules/mol/base/src/chain_type.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/base/src/image_state/image_state_factory.hh:31, from /<>/modules/img/base/src/image_state_fw.hh:30, from /<>/modules/img/base/src/image_impl.hh:33, from /<>/modules/img/base/src/image_impl.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/modules/img/base/src/image_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /<>/modules/mol/base/src/coord_frame.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /<>/modules/img/base/src/image_list.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /<>/modules/img/base/src/inverted_mask.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/base/src/image_list.hh:29, from /<>/modules/img/base/src/image_list.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/img/base/src/image_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/mask_base.hh:27, from /<>/modules/img/base/src/inverted_mask.hh:23, from /<>/modules/img/base/src/inverted_mask.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /<>/modules/mol/base/src/coord_group.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, from /<>/modules/mol/base/src/coord_frame.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /<>/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /<>/modules/img/base/src/map.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /<>/modules/img/base/src/mask_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /<>/modules/mol/base/src/in_mem_coord_source.hh:26, from /<>/modules/mol/base/src/coord_group.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /<>/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/base/src/map.hh:22, from /<>/modules/img/base/src/map.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/mask_base.hh:27, from /<>/modules/img/base/src/mask_base.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /<>/modules/img/base/src/mask_op.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /<>/modules/mol/base/src/editor_base.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /<>/modules/img/base/src/mask.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /<>/modules/mol/base/src/entity_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/mask_base.hh:27, from /<>/modules/img/base/src/composite_mask.hh:28, from /<>/modules/img/base/src/mask_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/scoped_ptr.hpp:23, from /usr/include/boost/scoped_ptr.hpp:13, from /usr/include/boost/smart_ptr.hpp:17, from /<>/modules/img/base/src/mask_base_fw.hh:23, from /<>/modules/img/base/src/mask_op.hh:24, from /<>/modules/img/base/src/mask_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/polygon_mask.hh:28, from /<>/modules/img/base/src/mask.hh:29, from /<>/modules/img/base/src/mask.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/mask.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/editor_base.hh:27, from /<>/modules/mol/base/src/editor_base.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/editor_base.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /<>/modules/img/base/src/observable.cc In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/editor_base.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /<>/modules/img/base/src/paste_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, from /<>/modules/mol/base/src/entity_base.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/entity_base.hh:22, from /<>/modules/mol/base/src/entity_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/observable.hh:31, from /<>/modules/img/base/src/observable.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/list:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/observable.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /<>/modules/mol/base/src/entity_handle.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /<>/modules/mol/base/src/entity_observer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/base/src/image_state/image_state_algorithm.hh:28, from /<>/modules/img/base/src/paste_impl.hh:24, from /<>/modules/img/base/src/paste_impl.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /<>/modules/img/base/src/peak.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /<>/modules/mol/base/src/entity_property_mapper.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/entity_impl.hh:28, from /<>/modules/mol/base/src/entity_handle.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/base/src/entity_handle.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/peak.hh:31, from /<>/modules/img/base/src/peak.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/img/base/src/peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /<>/modules/img/base/src/phase.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /<>/modules/img/base/src/physical_units.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/src/entity_property_mapper.hh:29, from /<>/modules/mol/base/src/entity_property_mapper.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/mol/base/src/entity_property_mapper.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/img/base/src/phase.cc: In member function ‘const ost::img::Phase ost::img::Phase::operator+=(const ost::img::Phase&)’: /<>/modules/img/base/src/phase.cc:49:47: note: parameter passing for argument of type ‘ost::img::Phase’ when C++17 is enabled changed to match C++14 in GCC 10.1 49 | const Phase Phase::operator+=(const Phase& rhs) | ^ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /<>/modules/img/base/src/pixel_sampling.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /<>/modules/img/base/src/point_list.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /<>/modules/mol/base/src/entity_view.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/point_list.hh:28, from /<>/modules/img/base/src/point_list.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/img/base/src/point.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/pixel_sampling.hh:32, from /<>/modules/img/base/src/pixel_sampling.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/modules/img/base/src/pixel_sampling.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /<>/modules/mol/base/src/entity_visitor.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /<>/modules/img/base/src/point.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /<>/modules/img/base/src/polygon_mask.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/mol/base/src/entity_view.hh:32, from /<>/modules/mol/base/src/entity_view.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/modules/mol/base/src/entity_view.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/entity_view.cc:40: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /<>/modules/mol/base/src/ics_editor.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/point.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/point.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /<>/modules/img/base/src/progress.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/polygon_mask.hh:28, from /<>/modules/img/base/src/polygon_mask.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/mol/base/src/entity_view.cc: In member function ‘std::pair ost::mol::EntityView::GetMinMax(const String&, ost::mol::Prop::Level) const’: /<>/modules/mol/base/src/entity_view.cc:662:62: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 662 | Prop::Level hint) const | ^~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /<>/modules/img/base/src/size.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/ics_editor.hh:26, from /<>/modules/mol/base/src/ics_editor.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/ics_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /<>/modules/img/base/src/spherical_mask.cc In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/ics_editor.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /<>/modules/mol/base/src/not_connected_error.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/img/base/src/vecmat.hh:33, from /<>/modules/img/base/src/point.hh:35, from /<>/modules/img/base/src/size.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/base/src/size.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/spherical_mask.hh:28, from /<>/modules/img/base/src/spherical_mask.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /<>/modules/img/base/src/mask_info_convert.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /<>/modules/img/base/src/image_state/image_state_factory.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /<>/modules/mol/base/src/property_id.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/base/src/image_state/image_state_factory.hh:31, from /<>/modules/img/base/src/image_state/image_state_factory.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data_types.hh:30, from /<>/modules/img/base/src/image_state/image_state_factory.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/img/base/src/mask_info_convert.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/deque:62, from /usr/include/c++/13/stack:62, from /<>/modules/img/base/src/mask_info_convert.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /<>/modules/mol/base/src/query.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /<>/modules/mol/base/src/query_error.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /<>/modules/mol/base/src/query_state.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /<>/modules/mol/base/src/residue_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/modules/mol/base/src/query.hh:39, from /<>/modules/mol/base/src/query.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/mol/base/src/query.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/modules/mol/base/src/query_state.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/query_state.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/residue_base.hh:22, from /<>/modules/mol/base/src/residue_base.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /<>/modules/mol/base/src/residue_handle.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /<>/modules/mol/base/src/residue_view.cc [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /<>/modules/img/base/src/image_state/index.cc [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /<>/modules/img/base/src/image_state/image_state_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/mol/base/src/residue_handle.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/residue_handle.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/mol/base/src/residue_view.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/modules/img/base/src/image_state/image_state_base.hh:34, from /<>/modules/img/base/src/image_state/image_state_base.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/modules/img/base/src/image_state/image_state_base_fw.hh:28, from /<>/modules/img/base/src/image_state/image_state_base.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /<>/modules/mol/base/src/surface_builder.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /<>/modules/mol/base/src/surface_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/modules/mol/base/src/surface_handle.hh:24, from /<>/modules/mol/base/src/surface_builder.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/surface_builder.hh:22, from /<>/modules/mol/base/src/surface_builder.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/modules/mol/base/src/surface_handle.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /<>/modules/mol/base/src/transfer_connectivity.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /<>/modules/mol/base/src/torsion_handle.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /<>/modules/mol/base/src/query_view_wrapper.cc [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /<>/modules/img/base/src/raster_image/raster_image.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/modules/mol/base/src/query.hh:39, from /<>/modules/mol/base/src/entity_handle.hh:26, from /<>/modules/mol/base/src/transfer_connectivity.hh:24, from /<>/modules/mol/base/src/transfer_connectivity.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/mol/base/src/module_config.hh:22, from /<>/modules/mol/base/src/transfer_connectivity.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /<>/modules/mol/base/src/torsion_handle.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /<>/modules/mol/base/src/torsion_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/base/src/query_view_wrapper.hh:24, from /<>/modules/mol/base/src/query_view_wrapper.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /<>/modules/mol/base/src/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /<>/modules/mol/base/src/view_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/base/src/raster_image/raster_image.hh:31, from /<>/modules/img/base/src/raster_image/raster_image.cc:38: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /<>/modules/mol/base/src/coord_source.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /<>/modules/mol/base/src/in_mem_coord_source.cc [ 13%] Linking CXX shared library ../../../../stage/lib/libost_img.so cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.5 -o ../../../../stage/lib/libost_img.so.2.5.0 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/src/view_op.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/mol/base/src/view_op.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/view_op.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5 ../../../../stage/lib/libost_img.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 13%] Built target ost_img make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/pymod /<>/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 13%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /<>/modules/base/pymod/wrap_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /<>/modules/mol/base/src/in_mem_coord_source.hh:26, from /<>/modules/mol/base/src/in_mem_coord_source.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/xcs_editor.hh:26, from /<>/modules/mol/base/src/coord_source.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/base/src/coord_source.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /<>/modules/mol/base/src/bounding_box.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /<>/modules/mol/base/src/xcs_editor.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/xcs_editor.hh:26, from /<>/modules/mol/base/src/xcs_editor.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/xcs_editor.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /<>/modules/mol/base/src/impl/atom_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /<>/modules/mol/base/src/impl/chain_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/src/bounding_box.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /<>/modules/mol/base/src/bounding_box.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/atom_impl.hh:25, from /<>/modules/mol/base/src/impl/atom_impl.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/atom_impl.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/atom_impl.hh:25, from /<>/modules/mol/base/src/impl/chain_impl.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/base/src/impl/chain_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/chain_impl.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /<>/modules/mol/base/src/impl/connector_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/connector_impl.hh:24, from /<>/modules/mol/base/src/impl/connector_impl.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /<>/modules/mol/base/src/impl/dihedral.cc In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/connector_impl.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /<>/modules/mol/base/src/impl/entity_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /<>/modules/mol/base/src/impl/fragment_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /<>/modules/mol/base/src/impl/dihedral.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:17, from /usr/include/boost/enable_shared_from_this.hpp:16, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/dihedral.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/fragment_impl.hh:22, from /<>/modules/mol/base/src/impl/fragment_impl.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/base/src/impl/entity_impl.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/modules/mol/base/src/impl/entity_impl.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/entity_impl.cc:40: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /<>/modules/mol/base/src/impl/query_ast.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /<>/modules/mol/base/src/impl/query_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/src/impl/query_impl.hh:36, from /<>/modules/mol/base/src/impl/query_impl.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/mol/base/src/impl/query_impl.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /<>/modules/mol/base/src/impl/residue_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /<>/modules/mol/base/src/impl/surface_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/mol/base/src/impl/residue_impl.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/base/src/impl/residue_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/base/src/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/residue_impl.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/modules/mol/base/src/impl/surface_impl.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /<>/modules/mol/base/src/impl/torsion_impl.cc [ 16%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /<>/modules/base/pymod/export_logger.cc [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /<>/modules/mol/base/src/impl/atom_prop.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /<>/modules/mol/base/src/impl/torsion_impl.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/base/src/impl/torsion_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/src/impl/torsion_impl.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 16%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /<>/modules/base/pymod/export_range.cc [ 16%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /<>/modules/base/pymod/export_units.cc [ 16%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.5 -o ../../../../stage/lib/libost_mol.so.2.5.0 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5 ../../../../stage/lib/libost_mol.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 16%] Built target ost_mol make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/src /<>/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /<>/modules/img/alg/src/anisotropic.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /<>/modules/img/alg/src/auto_correlate.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /<>/modules/img/alg/src/convolute.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/gaussian.hh:36, from /<>/modules/img/alg/src/anisotropic.hh:28, from /<>/modules/img/alg/src/anisotropic.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /<>/modules/img/alg/src/correlate.cc [ 17%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/_ost_base.so cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/fft.hh:27, from /<>/modules/img/alg/src/auto_correlate.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/alg/src/auto_correlate.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/settings.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/stutil.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/table.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/table_selector.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/xmlrunner.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/base/pymod/testutils.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 17%] Built target _ost_base make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/src /<>/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /<>/modules/seq/base/src/impl/sequence_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/convolute.hh:24, from /<>/modules/img/alg/src/convolute.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /<>/modules/img/alg/src/cross_correlate.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/correlate.hh:24, from /<>/modules/img/alg/src/correlate.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/seq/base/src/impl/sequence_impl.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /<>/modules/seq/base/src/impl/sequence_impl.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/cross_correlate.hh:27, from /<>/modules/img/alg/src/cross_correlate.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /<>/modules/img/alg/src/density_slice.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /<>/modules/img/alg/src/dft.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /<>/modules/img/alg/src/fft.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/density_slice.hh:28, from /<>/modules/img/alg/src/density_slice.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /<>/modules/img/alg/src/fourier_filters.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/dft.hh:24, from /<>/modules/img/alg/src/dft.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /<>/modules/seq/base/src/impl/sequence_list_impl.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/modules/img/alg/src/fft.cc:36: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/img/alg/src/fft.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /<>/modules/img/alg/src/gaussian.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /<>/modules/img/alg/src/gaussian_gradient_magnitude.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /<>/modules/img/alg/src/fourier_filters.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/fourier_filters.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/seq/base/src/impl/sequence_list_impl.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/gaussian.hh:36, from /<>/modules/img/alg/src/gaussian.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/gaussian.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, from /<>/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /<>/modules/img/alg/src/gaussian_laplacian.cc [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /<>/modules/seq/base/src/sequence_handle.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /<>/modules/img/alg/src/highest_peak_search_3d.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /<>/modules/img/alg/src/histogram.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/gaussian_laplacian.hh:28, from /<>/modules/img/alg/src/gaussian_laplacian.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/gaussian_laplacian.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/modules/seq/base/src/sequence_handle.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /<>/modules/seq/base/src/sequence_handle.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /<>/modules/img/alg/src/highest_peak_search_3d.cc:4: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /<>/modules/seq/base/src/aligned_region.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/stat.hh:30, from /<>/modules/img/alg/src/histogram.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/alg/src/histogram.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /<>/modules/img/alg/src/line_iterator.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /<>/modules/img/alg/src/local_sigma_threshold.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /<>/modules/img/alg/src/mask_image.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/alg/src/line_iterator.hh:29, from /<>/modules/img/alg/src/line_iterator.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /<>/modules/seq/base/src/aligned_region.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /<>/modules/seq/base/src/aligned_region.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /<>/modules/img/alg/src/normalizer.cc [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /<>/modules/seq/base/src/aligned_column.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/local_sigma_threshold.hh:23, from /<>/modules/img/alg/src/local_sigma_threshold.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/src/local_sigma_threshold.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/mask_image.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /<>/modules/img/alg/src/normalizer_factory.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/normalizer.hh:28, from /<>/modules/img/alg/src/normalizer.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /<>/modules/img/alg/src/norm_linear.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/modules/seq/base/src/aligned_column.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /<>/modules/img/alg/src/norm_log.cc [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /<>/modules/seq/base/src/sequence_list.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, from /<>/modules/img/alg/src/normalizer_factory.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/modules/img/alg/src/norm_linear.hh:28, from /<>/modules/img/alg/src/norm_linear.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/modules/img/alg/src/norm_log.hh:28, from /<>/modules/img/alg/src/norm_log.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /<>/modules/img/alg/src/norm_od.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/seq/base/src/sequence_list.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /<>/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /<>/modules/img/alg/src/power_spectrum.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/seq/base/src/sequence_list.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /<>/modules/img/alg/src/randomize.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/fft.hh:27, from /<>/modules/img/alg/src/power_spectrum.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/alg/src/power_spectrum.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/modules/img/alg/src/norm_od.hh:28, from /<>/modules/img/alg/src/norm_od.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /<>/modules/seq/base/src/alignment_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/randomize.hh:24, from /<>/modules/img/alg/src/randomize.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /<>/modules/img/alg/src/smooth_mask_image.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /<>/modules/img/alg/src/stat.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /<>/modules/img/alg/src/stat_min_max.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/modules/seq/base/src/alignment_handle.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /<>/modules/seq/base/src/alignment_handle.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/seq/base/src/alignment_handle.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/modules/seq/base/src/alignment_handle.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/smooth_mask_image.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/stat.hh:30, from /<>/modules/img/alg/src/stat.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/stat.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/stat_min_max.hh:30, from /<>/modules/img/alg/src/stat_min_max.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /<>/modules/img/alg/src/alg_transform.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /<>/modules/img/alg/src/alg_mirror.cc [ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /<>/modules/seq/base/src/sequence_op.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /<>/modules/img/alg/src/alg_shift.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/alg_transform.hh:24, from /<>/modules/img/alg/src/alg_transform.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/alg_mirror.hh:24, from /<>/modules/img/alg/src/alg_mirror.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/base/src/sequence_op.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/seq/base/src/sequence_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /<>/modules/img/alg/src/threshold.cc [ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /<>/modules/seq/base/src/views_from_sequences.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /<>/modules/img/alg/src/discrete_shrink.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/alg_shift.hh:24, from /<>/modules/img/alg/src/alg_shift.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /<>/modules/img/alg/src/transformation_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/threshold.hh:25, from /<>/modules/img/alg/src/threshold.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, from /<>/modules/seq/base/src/views_from_sequences.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /<>/modules/seq/base/src/views_from_sequences.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/src/discrete_shrink.hh:24, from /<>/modules/img/alg/src/discrete_shrink.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /<>/modules/img/alg/src/transformations.cc [ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /<>/modules/seq/base/src/profile_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/alg/src/transformation_base.hh:32, from /<>/modules/img/alg/src/transformation_base.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /<>/modules/img/alg/src/fractional_shift.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /<>/modules/img/alg/src/polar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/modules/img/alg/src/transformation_base.hh:32, from /<>/modules/img/alg/src/transformations.hh:31, from /<>/modules/img/alg/src/transformations.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/img/alg/src/transformations.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /<>/modules/img/alg/src/rscrosscorr.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /<>/modules/img/alg/src/fractional_shift.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/img/alg/src/fractional_shift.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/alg/src/polar.hh:24, from /<>/modules/img/alg/src/polar.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/img/alg/src/polar.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Linking CXX shared library ../../../../stage/lib/libost_seq.so cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_seq.so.2.5 -o ../../../../stage/lib/libost_seq.so.2.5.0 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5 ../../../../stage/lib/libost_seq.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 22%] Built target ost_seq make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/pymod /<>/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 22%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /<>/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /<>/modules/info/pymod/wrap_info.cc [ 22%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /<>/modules/img/alg/src/line_average.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/src/rscrosscorr.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/src /<>/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /<>/modules/db/src/sqlite_wrap.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /<>/modules/db/src/linear_indexer.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /<>/modules/db/src/binary_container.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/alg/src/line_average.hh:23, from /<>/modules/img/alg/src/line_average.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_img_alg.so.2.5 -o ../../../../stage/lib/libost_img_alg.so.2.5.0 CMakeFiles/ost_img_alg.dir/anisotropic.cc.o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o CMakeFiles/ost_img_alg.dir/convolute.cc.o CMakeFiles/ost_img_alg.dir/correlate.cc.o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o CMakeFiles/ost_img_alg.dir/density_slice.cc.o CMakeFiles/ost_img_alg.dir/dft.cc.o CMakeFiles/ost_img_alg.dir/fft.cc.o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o CMakeFiles/ost_img_alg.dir/gaussian.cc.o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o CMakeFiles/ost_img_alg.dir/histogram.cc.o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o CMakeFiles/ost_img_alg.dir/mask_image.cc.o CMakeFiles/ost_img_alg.dir/normalizer.cc.o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o CMakeFiles/ost_img_alg.dir/norm_log.cc.o CMakeFiles/ost_img_alg.dir/norm_od.cc.o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o CMakeFiles/ost_img_alg.dir/randomize.cc.o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o CMakeFiles/ost_img_alg.dir/stat.cc.o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o CMakeFiles/ost_img_alg.dir/threshold.cc.o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o CMakeFiles/ost_img_alg.dir/transformations.cc.o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o CMakeFiles/ost_img_alg.dir/polar.cc.o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o CMakeFiles/ost_img_alg.dir/line_average.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5 ../../../../stage/lib/libost_img_alg.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 24%] Built target ost_img_alg make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/src /<>/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /<>/modules/seq/alg/src/clip_alignment.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /<>/modules/db/src/extract_data_helper.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/info/pymod/wrap_info.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/info/pymod/wrap_info.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /<>/modules/seq/alg/src/conservation.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /<>/modules/seq/alg/src/clip_alignment.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /<>/modules/db/src/extract_data_helper.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /<>/modules/seq/alg/src/contact_prediction_score.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/modules/seq/alg/src/conservation.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_db.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.5 -o ../../../stage/lib/libost_db.so.2.5.0 CMakeFiles/ost_db.dir/sqlite_wrap.cc.o CMakeFiles/ost_db.dir/linear_indexer.cc.o CMakeFiles/ost_db.dir/binary_container.cc.o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_db.so.2.5 ../../../stage/lib/libost_db.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 24%] Built target ost_db make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/src /<>/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 24%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o cd /<>/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /<>/modules/bindings/src/wrap_tmalign.cc In file included from /usr/include/c++/13/string:54, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:27: In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’ at /<>/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:27: /usr/include/boost/variant/variant.hpp: In function ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’ at /<>/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/string:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’ at /<>/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /<>/modules/seq/alg/src/contact_weight_matrix.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/modules/seq/alg/src/contact_prediction_score.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/bindings/src/USalign/TMalign.h:7, from /<>/modules/bindings/src/wrap_tmalign.cc:20: /<>/modules/bindings/src/USalign/NW.h: In function ‘void NWDP_SE(bool**, double**, double**, double**, int, int, double, double, int*, int)’: /<>/modules/bindings/src/USalign/NW.h:275:9: warning: unused variable ‘int_min’ [-Wunused-variable] 275 | int int_min=L*(gap_open-1); | ^~~~~~~ /<>/modules/bindings/src/USalign/NW.h:287:9: warning: unused variable ‘k’ [-Wunused-variable] 287 | int k=0; | ^ In file included from /<>/modules/bindings/src/USalign/TMalign.h:9: /<>/modules/bindings/src/USalign/NWalign.h: In function ‘int NWalign_main(const char*, const char*, int, int, std::string&, std::string&, int, int*, int, int)’: /<>/modules/bindings/src/USalign/NWalign.h:415:41: warning: array subscript has type ‘char’ [-Wchar-subscripts] 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; | ~~~~~~~~^ /<>/modules/bindings/src/USalign/NWalign.h:415:52: warning: array subscript has type ‘char’ [-Wchar-subscripts] 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; | ~~~~~~~~^ /<>/modules/bindings/src/USalign/NWalign.h: In function ‘void get_seqID(const std::string&, const std::string&, std::string&, double&, int&)’: /<>/modules/bindings/src/USalign/NWalign.h:458:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 458 | for (int i=0;i>/modules/bindings/src/USalign/NWalign.h: In function ‘int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, std::vector, std::vector, int, int)’: /<>/modules/bindings/src/USalign/NWalign.h:697:14: warning: statement has no effect [-Wunused-value] 697 | for (i;i>/modules/bindings/src/USalign/NWalign.h:705:14: warning: statement has no effect [-Wunused-value] 705 | for (j;j>/modules/bindings/src/USalign/TMalign.h: In function ‘void make_sec(char*, double**, int, char*, std::string)’: /<>/modules/bindings/src/USalign/TMalign.h:878:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 878 | for (i=0;i>/modules/bindings/src/USalign/TMalign.h: In function ‘void output_pymol(std::string, std::string, std::string, double*, double (*)[3], int, int, int, int, const char*, const char*, const char*, const std::vector >&, const std::vector >&, std::string, std::string)’: /<>/modules/bindings/src/USalign/TMalign.h:1604:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘std::map, int>::mapped_type’ {aka ‘int’} [-Wsign-compare] 1604 | if (atom_site_pos==_atom_site["Cartn_x"]) /<>/modules/bindings/src/USalign/TMalign.h:1607:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘std::map, int>::mapped_type’ {aka ‘int’} [-Wsign-compare] 1607 | else if (atom_site_pos==_atom_site["Cartn_y"]) /<>/modules/bindings/src/USalign/TMalign.h:1610:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘std::map, int>::mapped_type’ {aka ‘int’} [-Wsign-compare] 1610 | else if (atom_site_pos==_atom_site["Cartn_z"]) /<>/modules/bindings/src/USalign/TMalign.h:1653:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1653 | for (i=1;i>/modules/bindings/src/USalign/TMalign.h:1655:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1655 | for (i=1;i>/modules/bindings/src/USalign/TMalign.h:1677:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1677 | for (i=0;i>/modules/bindings/src/USalign/TMalign.h:1716:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1716 | for (int p=0;p>/modules/bindings/src/USalign/TMalign.h: In function ‘void output_rasmol(std::string, std::string, std::string, double*, double (*)[3], int, int, int, int, const char*, const char*, const char*, const std::vector >&, const std::vector >&, std::string, std::string, int, int, double, int, double, double, double)’: /<>/modules/bindings/src/USalign/TMalign.h:1855:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1855 | for (i=1;i>/modules/bindings/src/USalign/TMalign.h:1857:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1857 | for (i=1;i>/modules/bindings/src/USalign/TMalign.h:1890:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1890 | for (i=0;i>/modules/bindings/src/USalign/TMalign.h:2162:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2162 | if (!mm_opt) for (i=1;i>/modules/bindings/src/USalign/TMalign.h:2372:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2372 | for (i=1;i>/modules/bindings/src/USalign/TMalign.h: In function ‘int TMalign_main(double**, double**, const char*, const char*, const char*, const char*, double*, double (*)[3], double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, std::vector >, double, double, int, int, bool, bool, bool, int, double)’: /<>/modules/bindings/src/USalign/TMalign.h:3289:12: warning: variable ‘Lnorm_d0’ set but not used [-Wunused-but-set-variable] 3289 | double Lnorm_d0; | ^~~~~~~~ /<>/modules/bindings/src/USalign/TMalign.h: In function ‘int CPalign_main(double**, double**, const char*, const char*, const char*, const char*, double*, double (*)[3], double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, std::vector >, double, double, int, int, bool, bool, bool, int, double)’: /<>/modules/bindings/src/USalign/TMalign.h:3467:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3467 | for (i=0;i>/modules/bindings/src/USalign/TMalign.h:3572:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3572 | for (i=0;i>/modules/bindings/src/USalign/TMalign.h: In function ‘bool output_cp(const std::string&, const std::string&, const std::string&, const std::string&, int, int&, int&, int&, int&)’: /<>/modules/bindings/src/USalign/TMalign.h:3606:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3606 | for (r=0;r>/modules/bindings/src/USalign/MMalign.h:2, from /<>/modules/bindings/src/wrap_tmalign.cc:21: /<>/modules/bindings/src/USalign/se.h: In function ‘int se_main(double**, double**, const char*, const char*, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, const std::vector >&, double, double, bool, bool, int, bool, int, int, int*, int)’: /<>/modules/bindings/src/USalign/se.h:52:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 52 | for (int r=0;r>/modules/bindings/src/USalign/se.h:222:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 222 | for (int r=0;r>/modules/bindings/src/USalign/se.h:44:9: warning: unused variable ‘i’ [-Wunused-variable] 44 | int i,j; | ^ /<>/modules/bindings/src/USalign/MMalign.h: In function ‘double homo_refined_greedy_search(double**, int*, int*, int, int, double**, double**, double, int, double**)’: /<>/modules/bindings/src/USalign/MMalign.h:440:12: warning: unused variable ‘TMnow’ [-Wunused-variable] 440 | double TMnow =0; | ^~~~~ /<>/modules/bindings/src/USalign/MMalign.h:441:12: warning: unused variable ‘TMmax’ [-Wunused-variable] 441 | double TMmax =0; | ^~~~~ /<>/modules/bindings/src/USalign/MMalign.h: In function ‘void clear_full_PDB_lines(std::vector > >, std::string)’: /<>/modules/bindings/src/USalign/MMalign.h:670:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 670 | for (chain_i=0;chain_i>/modules/bindings/src/USalign/MMalign.h:673:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 673 | for (a=0;a>/modules/bindings/src/USalign/MMalign.h:687:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 687 | for (a=0;a>/modules/bindings/src/USalign/MMalign.h: In function ‘void output_dock(const std::vector >&, int, int, int, std::string, int, double**, const std::string&)’: /<>/modules/bindings/src/USalign/MMalign.h:1010:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1010 | for (a=0;a>/modules/bindings/src/USalign/MMalign.h: In function ‘int copy_chain_pair_data(const std::vector > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, std::vector > >&, std::vector > >&, int*, int*, std::vector >&)’: /<>/modules/bindings/src/USalign/MMalign.h:1166:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1166 | for (i=0;i>/modules/bindings/src/USalign/MMalign.h: In function ‘void copy_chain_assign_data(int, int, std::vector >&, std::vector > >&, std::vector > >&, int*, int*, double**, std::vector > >&, std::vector > >&, int*, int*, double**)’: /<>/modules/bindings/src/USalign/MMalign.h:1590:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1590 | for (i=0;i>/modules/bindings/src/USalign/MMalign.h: In function ‘int TMalign_dimer_main(double**, double**, const char*, const char*, const char*, const char*, double*, double (*)[3], double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, bool**, std::vector >, double, double, int, int, bool, bool, bool, int, double)’: /<>/modules/bindings/src/USalign/MMalign.h:2528:12: warning: variable ‘Lnorm_d0’ set but not used [-Wunused-but-set-variable] 2528 | double Lnorm_d0; | ^~~~~~~~ /<>/modules/bindings/src/USalign/MMalign.h: In function ‘void MMalign_dimer(double&, const std::vector > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, int, int, double**, std::vector > >&, std::vector > >&, int*, int*, std::vector >&, double, bool)’: /<>/modules/bindings/src/USalign/MMalign.h:2680:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2680 | for (c=0;c>/modules/bindings/src/USalign/MMalign.h: In function ‘void writeTrimComplex(std::vector > >&, std::vector >&, std::vector&, std::vector >&, std::vector&, const std::string&, std::string)’: /<>/modules/bindings/src/USalign/MMalign.h:2979:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2979 | for (c=0;c>/modules/bindings/src/USalign/MMalign.h: In function ‘void output_dock_rotation_matrix(const char*, const std::vector >&, const std::vector >&, double**, int*)’: /<>/modules/bindings/src/USalign/MMalign.h:3016:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3016 | for (i=0;i>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /<>/modules/seq/alg/src/distance_map.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /<>/modules/bindings/src/wrap_tmalign.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh: At global scope: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /<>/modules/bindings/src/USalign/param_set.h:6, from /<>/modules/bindings/src/USalign/TMalign.h:6: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /<>/modules/seq/alg/src/entropy.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/alg/src/distance_map.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /<>/modules/seq/alg/src/distance_map.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/seq/alg/src/entropy.hh:24, from /<>/modules/seq/alg/src/entropy.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/seq/alg/src/entropy.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/global_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/global_align.cc.o -c /<>/modules/seq/alg/src/global_align.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /<>/modules/seq/alg/src/ins_del.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/seq/alg/src/impl/align_impl.hh:22, from /<>/modules/seq/alg/src/global_align.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /<>/modules/seq/alg/src/ins_del.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /<>/modules/seq/alg/src/local_align.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /<>/modules/seq/alg/src/merge_pairwise_alignments.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/seq/alg/src/impl/align_impl.hh:22, from /<>/modules/seq/alg/src/local_align.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/seq/alg/src/local_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/seq/alg/src/merge_pairwise_alignments.hh:22, from /<>/modules/seq/alg/src/merge_pairwise_alignments.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/seq/alg/src/merge_pairwise_alignments.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -c /<>/modules/seq/alg/src/pair_subst_weight_matrix.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /<>/modules/seq/alg/src/semiglobal_align.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/seq/alg/src/impl/align_impl.hh:22, from /<>/modules/seq/alg/src/semiglobal_align.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/seq/alg/src/semiglobal_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/bindings/src/USalign/MMalign.h: In function ‘int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)’: /<>/modules/bindings/src/USalign/MMalign.h:2941:43: warning: ‘dinter’ may be used uninitialized [-Wmaybe-uninitialized] 2941 | dinter_vec.push_back(make_pair(dinter,r1)); | ~~~~~~~~~^~~~~~~~~~~ /<>/modules/bindings/src/USalign/MMalign.h:2894:12: note: ‘dinter’ was declared here 2894 | double dinter; | ^~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /<>/modules/seq/alg/src/sequence_identity.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /<>/modules/seq/alg/src/sequence_similarity.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /<>/modules/seq/alg/src/sequence_identity.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /<>/modules/seq/alg/src/sequence_similarity.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/info/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 25%] Built target _ost_info make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/src /<>/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /<>/modules/conop/src/processor.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -c /<>/modules/seq/alg/src/subst_weight_matrix.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/variance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -c /<>/modules/seq/alg/src/variance_map.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -c /<>/modules/seq/alg/src/hmm_pseudo_counts.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/conop/src/processor.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/conop/src/processor.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/alg/src/variance_map.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/seq/alg/src/variance_map.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /<>/modules/seq/alg/src/variance_map.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/seq/alg/src/hmm_pseudo_counts.cc: In static member function ‘static ost::seq::alg::ContextProfileDBPtr ost::seq::alg::ContextProfileDB::FromCRF(const String&)’: /<>/modules/seq/alg/src/hmm_pseudo_counts.cc:146:56: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 146 | if(boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/modules/seq/alg/src/hmm_pseudo_counts.cc:4: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -c /<>/modules/seq/alg/src/hmm_score.cc /<>/modules/bindings/src/USalign/NWalign.h: In function ‘int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, int)’: /<>/modules/bindings/src/USalign/NWalign.h:545:21: warning: ‘invmap’ may be used uninitialized [-Wmaybe-uninitialized] 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 | mol_type, invmap, 0, glocal); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/modules/bindings/src/USalign/NWalign.h:535:14: note: ‘invmap’ was declared here 535 | int *invmap; | ^~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o -MF CMakeFiles/ost_conop.dir/amino_acids.cc.o.d -o CMakeFiles/ost_conop.dir/amino_acids.cc.o -c /<>/modules/conop/src/amino_acids.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, from /<>/modules/seq/alg/src/hmm_score.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /<>/modules/conop/src/conop.cc /<>/modules/bindings/src/wrap_tmalign.cc: In function ‘ost::bindings::MMAlignResult ost::bindings::WrappedMMAlign(const std::vector&, const std::vector&, const ost::seq::SequenceList&, const ost::seq::SequenceList&, const std::vector&, const std::vector&, bool)’: /<>/modules/bindings/src/wrap_tmalign.cc:896:36: warning: ‘seqy’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/modules/bindings/src/wrap_tmalign.cc:548:18: note: ‘seqy’ was declared here 548 | char *seqx, *seqy; // for the protein sequence | ^~~~ /<>/modules/bindings/src/wrap_tmalign.cc:896:36: warning: ‘secx’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/modules/bindings/src/wrap_tmalign.cc:549:11: note: ‘secx’ was declared here 549 | char *secx, *secy; // for the secondary structure | ^~~~ /<>/modules/bindings/src/wrap_tmalign.cc:896:36: warning: ‘secy’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/modules/bindings/src/wrap_tmalign.cc:549:18: note: ‘secy’ was declared here 549 | char *secx, *secy; // for the secondary structure | ^~~~ /<>/modules/bindings/src/wrap_tmalign.cc:896:36: warning: ‘seqx’ may be used uninitialized [-Wmaybe-uninitialized] 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | sequence, d0_scale, fast_opt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/modules/bindings/src/wrap_tmalign.cc:548:11: note: ‘seqx’ was declared here 548 | char *seqx, *seqy; // for the protein sequence | ^~~~ [ 25%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.5 -o ../../../../stage/lib/libost_seq_alg.so.2.5.0 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5 ../../../../stage/lib/libost_seq_alg.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 25%] Built target ost_seq_alg make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/pymod /<>/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 25%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /<>/modules/img/base/pymod/export_data.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/conop/src/amino_acids.hh:26, from /<>/modules/conop/src/amino_acids.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/set:62, from /<>/modules/conop/src/amino_acids.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/conop/src/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/conop/src/conop.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/conop/src/conop.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -c /<>/modules/conop/src/minimal_compound_lib.cc [ 26%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /<>/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.5 -o ../../../stage/lib/libost_bindings.so.2.5.0 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.5.0 ../../../stage/lib/libost_bindings.so.2.5 ../../../stage/lib/libost_bindings.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 26%] Built target ost_bindings make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /<>/modules/mol/base/pymod/export_atom.cc [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib_base.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -c /<>/modules/conop/src/compound_lib_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/conop/src/compound_lib_base.hh:5, from /<>/modules/conop/src/minimal_compound_lib.hh:5, from /<>/modules/conop/src/minimal_compound_lib.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/conop/src/compound.hh:22, from /<>/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/modules/img/base/pymod/export_data.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_data.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/conop/src/compound_lib_base.hh:5, from /<>/modules/conop/src/compound_lib_base.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/conop/src/compound.hh:22, from /<>/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /<>/modules/conop/src/heuristic.cc [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /<>/modules/img/base/pymod/export_data_algorithm.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_atom.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_atom.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/conop/src/heuristic.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/conop/src/heuristic.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o -MF CMakeFiles/ost_conop.dir/diag.cc.o.d -o CMakeFiles/ost_conop.dir/diag.cc.o -c /<>/modules/conop/src/diag.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/base/pymod/export_data_algorithm.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/conop/src/diag.hh:23, from /<>/modules/conop/src/diag.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /<>/modules/conop/src/diag.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -MF CMakeFiles/ost_conop.dir/rule_based.cc.o.d -o CMakeFiles/ost_conop.dir/rule_based.cc.o -c /<>/modules/conop/src/rule_based.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/conop/src/rule_based.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/conop/src/rule_based.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /<>/modules/img/base/pymod/export_extent.cc [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /<>/modules/conop/src/model_check.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/modules/conop/src/model_check.hh:4, from /<>/modules/conop/src/model_check.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/conop/src/model_check.cc:2: /<>/modules/conop/src/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/base/pymod/wrap_extent_iterator.hh:34, from /<>/modules/img/base/pymod/export_extent.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_extent.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /<>/modules/conop/src/compound.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /<>/modules/mol/base/pymod/export_atom_view.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /<>/modules/conop/src/compound_lib.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -MF CMakeFiles/ost_conop.dir/ring_finder.cc.o.d -o CMakeFiles/ost_conop.dir/ring_finder.cc.o -c /<>/modules/conop/src/ring_finder.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/conop/src/compound_lib_base.hh:5, from /<>/modules/conop/src/compound_lib.hh:27, from /<>/modules/conop/src/compound_lib.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/conop/src/compound_lib.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /<>/modules/img/base/pymod/export_image_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/conop/src/ring_finder.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:24: In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_atom_view.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’ at /<>/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function ‘int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /<>/modules/img/base/pymod/export_peak.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/base/pymod/export_image_handle.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.5 -o ../../../stage/lib/libost_conop.so.2.5.0 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5 ../../../stage/lib/libost_conop.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 27%] Built target ost_conop make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/src /<>/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /<>/modules/mol/alg/src/svd_superpose.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/peak.hh:31, from /<>/modules/img/base/pymod/export_peak.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /<>/modules/mol/base/pymod/export_bond.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /<>/modules/mol/alg/src/svd_superpose.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /<>/modules/img/base/pymod/export_phase.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_bond.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_bond.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /<>/modules/img/base/pymod/export_point.cc In file included from /usr/include/boost/python/type_id.hpp:11, from /usr/include/boost/python/instance_holder.hpp:11, from /usr/include/boost/python/object/pointer_holder.hpp:14, from /usr/include/boost/python/to_python_indirect.hpp:10, from /usr/include/boost/python/converter/arg_to_python.hpp:10, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_phase.cc:25: /usr/include/boost/operators.hpp: In instantiation of ‘ost::img::Phase boost::operators_impl::operator+(const ost::img::Phase&, const ost::img::Phase&)’: /usr/include/boost/python/operators.hpp:212:1: required from ‘static PyObject* boost::python::detail::operator_l::apply::execute(lhs&, const rhs&) [with L = ost::img::Phase; R = ost::img::Phase; PyObject = _object; lhs = ost::img::Phase; rhs = ost::img::Phase]’ /usr/include/boost/python/operators.hpp:154:15: required from ‘void boost::python::detail::operator_::visit(ClassT&) const [with ClassT = boost::python::class_; boost::python::detail::operator_id id = boost::python::detail::op_add; L = boost::python::self_ns::self_t; R = boost::python::self_ns::self_t]’ /usr/include/boost/python/def_visitor.hpp:31:34: required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >; classT = boost::python::class_]’ /usr/include/boost/python/def_visitor.hpp:67:34: required from ‘void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_; DerivedVisitor = boost::python::detail::operator_]’ /usr/include/boost/python/class.hpp:221:22: required from ‘boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::detail::operator_; W = ost::img::Phase; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_]’ /<>/modules/img/base/pymod/export_phase.cc:40:9: required from here /usr/include/boost/operators.hpp:269:1: note: parameter passing for argument of type ‘ost::img::Phase’ when C++17 is enabled changed to match C++14 in GCC 10.1 269 | BOOST_BINARY_OPERATOR_COMMUTATIVE( addable, + ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /<>/modules/img/base/pymod/export_progress.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /<>/modules/img/base/pymod/export_point.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_point.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /<>/modules/img/base/pymod/export_raster_image.cc [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /<>/modules/mol/alg/src/clash_score.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /<>/modules/mol/base/pymod/export_chain.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/alg/src/clash_score.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /<>/modules/img/base/pymod/export_size.cc [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /<>/modules/mol/alg/src/sec_structure_segments.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, from /<>/modules/img/base/pymod/export_raster_image.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/sec_structure_segments.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /<>/modules/img/base/pymod/export_mask.cc [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /<>/modules/mol/alg/src/local_dist_diff_test.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_chain.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_chain.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/modules/img/base/pymod/export_size.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_size.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/local_dist_diff_test.cc:4: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /<>/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/mol/alg/src/local_dist_diff_test.hh:24, from /<>/modules/mol/alg/src/local_dist_diff_test.cc:6: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/alg/src/local_dist_diff_test.hh:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /<>/modules/img/base/pymod/export_image_list.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/mask.hh:29, from /<>/modules/img/base/pymod/export_mask.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /<>/modules/img/base/pymod/export_map.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/base/pymod/export_image_list.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_image_list.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/modules/img/base/pymod/export_map.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/export_map.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /<>/modules/mol/alg/src/distance_test_common.cc [ 29%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /<>/modules/img/base/pymod/wrap_img.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, from /<>/modules/mol/alg/src/distance_test_common.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /<>/modules/mol/alg/src/distance_rmsd_test.cc [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /<>/modules/mol/alg/src/superpose_frames.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/distance_rmsd_test.cc:2: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/alg/src/distance_rmsd_test.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /<>/modules/mol/alg/src/distance_rmsd_test.cc:3: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/modules/img/base/pymod/wrap_img.cc:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/base/pymod/wrap_img.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /<>/modules/mol/base/pymod/export_chain_view.cc [ 29%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/img/base/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 29%] Built target _ost_img make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/src /<>/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /<>/modules/gfx/src/bitmap_io.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/superpose_frames.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /<>/modules/mol/alg/src/superpose_frames.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/string:54: In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’ at /<>/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /<>/modules/gfx/src/exporter.cc [ 29%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /<>/modules/mol/alg/src/filter_clashes.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_chain_view.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/exporter.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/filter_clashes.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/alg/src/filter_clashes.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/alg/src/filter_clashes.cc:24: /<>/modules/mol/alg/src/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/modules/mol/alg/src/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /<>/modules/gfx/src/collada_exporter.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/scene.hh:37, from /<>/modules/gfx/src/collada_exporter.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /<>/modules/gfx/src/color.cc [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /<>/modules/mol/alg/src/construct_cbeta.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/color.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/modules/gfx/src/color.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /<>/modules/gfx/src/primitives.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/construct_cbeta.cc:4: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /<>/modules/mol/alg/src/trajectory_analysis.cc [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /<>/modules/mol/base/pymod/export_coord_group.cc [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /<>/modules/mol/alg/src/structure_analysis.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /<>/modules/gfx/src/primitives.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/modules/gfx/src/gl_helper.hh:36, from /<>/modules/gfx/src/primitives.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /<>/modules/gfx/src/entity.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/mol/alg/src/trajectory_analysis.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/structure_analysis.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /<>/modules/mol/alg/src/consistency_checks.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/gfx/src/entity.cc:36: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/gfx/src/entity.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /<>/modules/mol/alg/src/pdbize.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh:31, from /<>/modules/gfx/src/entity.cc:39: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /<>/modules/gfx/src/entity.cc:52: /<>/modules/gfx/src/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /<>/modules/mol/base/pymod/export_coord_group.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gfx/src/entity.cc: In member function ‘void ost::gfx::Entity::ColorBy(const String&, const ost::gfx::Color&, const ost::gfx::Color&, ost::mol::Prop::Level)’: /<>/modules/gfx/src/entity.cc:965:72: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 965 | std::pair minmax = this->GetView().GetMinMax(prop, level); | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/mol/alg/src/consistency_checks.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/alg/src/consistency_checks.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/alg/src/pdbize.hh:22, from /<>/modules/mol/alg/src/pdbize.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/mol/alg/src/pdbize.hh:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /<>/modules/mol/alg/src/adjacency_bitmap.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /<>/modules/mol/alg/src/adjacency_bitmap.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_factory.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/mol/alg/src/adjacency_bitmap.hh:9, from /<>/modules/mol/alg/src/adjacency_bitmap.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /<>/modules/mol/alg/src/contact_overlap.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /<>/modules/gfx/src/symmetry_node.cc [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /<>/modules/mol/base/pymod/export_coord_frame.cc [ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /<>/modules/mol/alg/src/domain_find.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/symmetry_node.hh:22, from /<>/modules/gfx/src/symmetry_node.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/modules/gfx/src/gl_helper.hh:36, from /<>/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/src/contact_overlap.cc:2: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/mol/alg/src/contact_overlap.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/mol/alg/src/contact_overlap.cc:3: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /<>/modules/gfx/src/gfx_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /<>/modules/mol/alg/src/domain_find.cc:3: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/thread/exceptions.hpp:20, from /usr/include/boost/thread/pthread/thread_data.hpp:10, from /usr/include/boost/thread/thread_only.hpp:17, from /usr/include/boost/thread/thread.hpp:12, from /usr/include/boost/thread.hpp:13, from /<>/modules/mol/alg/src/domain_find.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/mol/alg/src/domain_find.cc:9: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/gfx_object_base.hh:26, from /<>/modules/gfx/src/gfx_object.hh:40, from /<>/modules/gfx/src/gfx_node.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/bind/mem_fn.hpp:25, from /usr/include/boost/bind/bind.hpp:26, from /<>/modules/gfx/src/gfx_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/modules/mol/base/pymod/export_coord_frame.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/string:54: In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’ at /<>/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’ at /<>/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’ at /<>/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::CalcContactNodeDegree(const ContactList&)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’ at /<>/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /<>/modules/gfx/src/gfx_object.cc [ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /<>/modules/mol/alg/src/similarity_matrix.cc [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /<>/modules/mol/base/pymod/export_editors.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/mol/alg/src/similarity_matrix.hh:7, from /<>/modules/mol/alg/src/similarity_matrix.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/alg/src/domain_find.cc:11: In member function ‘void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)’, inlined from ‘ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, inlined from ‘static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)’ at /<>/modules/mol/alg/src/domain_find.cc:363:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: ‘*(uint64_t*)’ may be used uninitialized [-Wmaybe-uninitialized] 109 | data_[byte_index] &= ~(one << bit_index); | ~~~~~~~~~~~~~~~~^ [ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /<>/modules/mol/alg/src/accessibility.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /<>/modules/gfx/src/gfx_object.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /<>/modules/mol/alg/src/sec_struct.cc In file included from /<>/modules/gfx/src/gfx_object_base.hh:34, from /<>/modules/gfx/src/gfx_object.hh:40, from /<>/modules/gfx/src/gfx_object.cc:32: /<>/modules/gfx/src/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/modules/gfx/src/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /<>/modules/mol/alg/src/sec_struct.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /<>/modules/mol/alg/src/accessibility.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/mol/alg/src/accessibility.cc:312:40: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float; _T2 = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/mol/alg/src/sec_struct.cc:567:31: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_editors.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_editors.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/pymod/export_editors.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /<>/modules/gfx/src/gfx_prim.cc In constructor ‘{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)’, inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]’ at /usr/include/c++/13/bits/vector.tcc:117:30, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)’ at /<>/modules/mol/alg/src/sec_struct.cc:87:33: /<>/modules/mol/alg/src/sec_struct.cc:10:8: warning: ‘.{anonymous}::ExtendedBridge::parallel’ may be used uninitialized [-Wmaybe-uninitialized] 10 | struct ExtendedBridge { | ^~~~~~~~~~~~~~ /<>/modules/mol/alg/src/sec_struct.cc: In function ‘bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)’: /<>/modules/mol/alg/src/sec_struct.cc:87:49: note: ‘’ declared here 87 | extended_bridges.push_back(ExtendedBridge()); | ^ In constructor ‘{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)’, inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]’ at /usr/include/c++/13/bits/vector.tcc:468:28, inlined from ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]’ at /usr/include/c++/13/bits/vector.tcc:123:21, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)’ at /<>/modules/mol/alg/src/sec_struct.cc:87:33: /<>/modules/mol/alg/src/sec_struct.cc:10:8: warning: ‘.{anonymous}::ExtendedBridge::parallel’ may be used uninitialized [-Wmaybe-uninitialized] 10 | struct ExtendedBridge { | ^~~~~~~~~~~~~~ /<>/modules/mol/alg/src/sec_struct.cc: In function ‘bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)’: /<>/modules/mol/alg/src/sec_struct.cc:87:49: note: ‘’ declared here 87 | extended_bridges.push_back(ExtendedBridge()); | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/gfx_prim.hh:28, from /<>/modules/gfx/src/gfx_prim.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /<>/modules/mol/alg/src/nonstandard.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /<>/modules/gfx/src/gfx_test_object.cc In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:24: In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:27: /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/mol/alg/src/nonstandard.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/mol/alg/src/nonstandard.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/gfx_object_base.hh:26, from /<>/modules/gfx/src/gfx_object.hh:40, from /<>/modules/gfx/src/gfx_test_object.hh:28, from /<>/modules/gfx/src/gfx_test_object.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/operations.hpp:20, from /<>/modules/gfx/src/gfx_test_object.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gfx/src/gfx_object.hh:124:31: warning: ‘virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const’ was hidden [-Woverloaded-virtual=] 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; | ^~~~~~~~~~~~~~ /<>/modules/gfx/src/gfx_test_object.hh:40:31: note: by ‘virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const’ 40 | virtual geom::AlignedCuboid GetBoundingBox() const; | ^~~~~~~~~~~~~~ [ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /<>/modules/mol/alg/src/molck.cc In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’ at /<>/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /<>/modules/gfx/src/input.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /<>/modules/gfx/src/prim_list.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/mol/alg/src/molck.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /<>/modules/mol/alg/src/find_membrane.cc In file included from /<>/modules/mol/alg/src/molck.cc:4: /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /<>/modules/mol/base/pymod/export_entity.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/scene.hh:37, from /<>/modules/gfx/src/prim_list.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /<>/modules/gfx/src/prim_list.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /<>/modules/mol/alg/src/find_membrane.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /<>/modules/mol/alg/src/entity_to_density.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /<>/modules/gfx/src/scene.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/base/pymod/export_entity.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /<>/modules/mol/base/pymod/export_entity.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, from /<>/modules/mol/alg/src/entity_to_density.cc:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/mol/alg/src/entity_to_density.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/scene.cc:40: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/gfx/src/scene.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/gfx/src/scene.cc:49: /<>/modules/gfx/src/gfx_object.hh:124:31: warning: ‘virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const’ was hidden [-Woverloaded-virtual=] 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; | ^~~~~~~~~~~~~~ In file included from /<>/modules/gfx/src/scene.cc:50: /<>/modules/gfx/src/gfx_test_object.hh:40:31: note: by ‘virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const’ 40 | virtual geom::AlignedCuboid GetBoundingBox() const; | ^~~~~~~~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /<>/modules/gfx/src/selection.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gfx/src/selection.hh:26, from /<>/modules/gfx/src/selection.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /<>/modules/gfx/src/surface.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /<>/modules/gfx/src/gradient.cc In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:24: In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’ at /<>/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’ at /<>/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’ at /<>/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gfx/src/surface.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/modules/gfx/src/surface.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/gradient.hh:28, from /<>/modules/gfx/src/gradient.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/gfx/src/gradient.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/atom_scattering_properties.txt /<>/obj-aarch64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/stereo_chemical_props.txt /<>/obj-aarch64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.5 -o ../../../../stage/lib/libost_mol_alg.so.2.5.0 CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o CMakeFiles/ost_mol_alg.dir/molck.cc.o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so In file included from /<>/modules/gfx/src/gfx_object_base.hh:34, from /<>/modules/gfx/src/gfx_object.hh:40, from /<>/modules/gfx/src/surface.hh:32, from /<>/modules/gfx/src/surface.cc:28: /<>/modules/gfx/src/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/modules/gfx/src/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 34%] Built target ost_mol_alg make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /<>/modules/img/alg/pymod/wrap_alg.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /<>/modules/gfx/src/gradient_manager.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/gfx/src/gradient_manager.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/operations.hpp:20, from /<>/modules/gfx/src/gradient_manager.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /<>/modules/gfx/src/vertex_array.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /<>/modules/gfx/src/vertex_array_helper.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, from /<>/modules/img/alg/pymod/wrap_alg.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/vertex_array.hh:34, from /<>/modules/gfx/src/vertex_array.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /<>/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/vertex_array_helper.hh:23, from /<>/modules/gfx/src/vertex_array_helper.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gfx/src/vertex_array.cc:1311:8: warning: ‘geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)’ defined but not used [-Wunused-function] 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) | ^~~~~~~~~~~~~~~~ /<>/modules/gfx/src/vertex_array.cc:1239:8: warning: ‘void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)’ defined but not used [-Wunused-function] 1239 | void render_aalines(AALineList& line_list, float w, float r) | ^~~~~~~~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /<>/modules/gfx/src/material.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/material.hh:22, from /<>/modules/gfx/src/material.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/iterator:61, from /usr/include/boost/operators.hpp:98, from /<>/modules/gfx/src/color.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /<>/modules/gfx/src/povray.cc [ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /<>/modules/mol/base/pymod/export_entity_view.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/povray.hh:31, from /<>/modules/gfx/src/povray.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/gfx/src/povray.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /<>/modules/gfx/src/gost_exporter.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/color.hh:31, from /<>/modules/gfx/src/scene.hh:37, from /<>/modules/gfx/src/gost_exporter.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/gfx/src/gost_exporter.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /<>/modules/gfx/src/texture.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/base/pymod/export_entity_view.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /<>/modules/gfx/src/color_ops/color_op.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /<>/modules/gfx/src/color_ops/by_element_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /<>/modules/gfx/src/color_ops/color_op.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/gfx/src/color_ops/by_element_color_op.hh:24, from /<>/modules/gfx/src/color_ops/by_element_color_op.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/modules/gfx/src/color_ops/by_element_color_op.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /<>/modules/gfx/src/color_ops/by_chain_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gfx/src/color_ops/by_element_color_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /<>/modules/gfx/src/color_ops/uniform_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/gfx/src/color_ops/by_chain_color_op.hh:23, from /<>/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /<>/modules/gfx/src/color_ops/by_chain_color_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gfx/src/color_ops/by_chain_color_op.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/color_ops/uniform_color_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /<>/modules/gfx/src/color_ops/uniform_color_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /<>/modules/gfx/src/color_ops/gradient_color_op.cc [ 37%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /<>/modules/img/alg/pymod/export_filter.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /<>/modules/gfx/src/color_ops/entity_view_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/color_ops/gradient_color_op.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /<>/modules/mol/base/pymod/export_property_id.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /<>/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, from /<>/modules/img/alg/pymod/export_filter.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/alg/pymod/export_filter.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /<>/modules/gfx/src/color_ops/gradient_level_color_op.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, from /<>/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/surface.hh:32, from /<>/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/surface.hh:102:8: note: by ‘ost::gfx::Surface::Apply’ 102 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /<>/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /<>/modules/gfx/src/impl/entity_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_property_id.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /<>/modules/gfx/src/impl/entity_detail.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /<>/modules/gfx/src/impl/entity_renderer.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /<>/modules/gfx/src/impl/entity_renderer.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /<>/modules/mol/base/pymod/export_query.cc [ 37%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /<>/modules/img/alg/pymod/export_normalizer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/impl/entity_detail.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, from /<>/modules/gfx/src/impl/entity_detail.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /<>/modules/gfx/src/impl/cartoon_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/impl/cartoon_renderer.hh:27, from /<>/modules/gfx/src/impl/cartoon_renderer.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/mol/base/pymod/export_query.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_query.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /<>/modules/gfx/src/impl/custom_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /<>/modules/img/alg/pymod/export_normalizer.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, from /<>/modules/gfx/src/impl/custom_renderer.hh:22, from /<>/modules/gfx/src/impl/custom_renderer.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /<>/modules/mol/base/pymod/export_residue.cc [ 37%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /<>/modules/img/alg/pymod/export_transcendentals.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /<>/modules/gfx/src/impl/cpk_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /<>/modules/gfx/src/impl/cpk_renderer.hh:24, from /<>/modules/gfx/src/impl/cpk_renderer.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/modules/gfx/src/impl/cpk_renderer.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_residue.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_residue.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, from /<>/modules/img/alg/pymod/export_transcendentals.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/alg/pymod/export_transcendentals.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /<>/modules/gfx/src/impl/cpk_renderer.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /<>/modules/gfx/src/impl/debug_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /<>/modules/gfx/src/impl/debug_renderer.hh:22, from /<>/modules/gfx/src/impl/debug_renderer.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /<>/modules/img/alg/pymod/export_polar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/QR:11, from /usr/include/eigen3/Eigen/SVD:11, from /<>/modules/gfx/src/impl/cartoon_renderer.cc:26: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const float*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /<>/modules/gfx/src/impl/simple_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, from /<>/modules/img/alg/pymod/export_polar.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/img/alg/pymod/export_polar.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/impl/simple_renderer.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /<>/modules/gfx/src/impl/simple_renderer.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gfx/src/impl/simple_renderer.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 39%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/img/alg/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 39%] Built target _ost_img_alg make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/src /<>/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 39%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o -MF CMakeFiles/ost_io.dir/io_manager.cc.o.d -o CMakeFiles/ost_io.dir/io_manager.cc.o -c /<>/modules/io/src/io_manager.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /<>/modules/gfx/src/impl/sline_renderer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/io_manager.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /<>/modules/gfx/src/impl/sline_renderer.hh:29, from /<>/modules/gfx/src/impl/sline_renderer.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, from /<>/modules/gfx/src/impl/sline_renderer.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /<>/modules/gfx/src/impl/line_trace_renderer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /<>/modules/gfx/src/impl/backbone_trace.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /<>/modules/gfx/src/impl/line_trace_renderer.hh:29, from /<>/modules/gfx/src/impl/line_trace_renderer.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gfx/src/impl/backbone_trace.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -MF CMakeFiles/ost_io.dir/convert.cc.o.d -o CMakeFiles/ost_io.dir/convert.cc.o -c /<>/modules/io/src/convert.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:35, from /<>/modules/gfx/src/impl/backbone_trace.hh:29, from /<>/modules/gfx/src/impl/backbone_trace.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /<>/modules/gfx/src/impl/connect_renderer_base.cc [ 39%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /<>/modules/io/src/io_utils.cc [ 39%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -c /<>/modules/io/src/mol/entity_io_crd_handler.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /<>/modules/gfx/src/impl/trace_renderer_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/impl/connect_renderer_base.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/impl/trace_renderer_base.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/entity_io_crd_handler.cc:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/entity_io_crd_handler.cc: In constructor ‘ost::io::CRDReader::CRDReader(const boost::filesystem::path&)’: /<>/modules/io/src/mol/entity_io_crd_handler.cc:63:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 63 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/entity_io_crd_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /<>/modules/gfx/src/impl/mapped_property.cc [ 39%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /<>/modules/mol/base/pymod/export_residue_view.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /<>/modules/gfx/src/impl/mapped_property.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /<>/modules/gfx/src/impl/tabulated_trig.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /<>/modules/gfx/src/impl/trace_renderer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /<>/modules/gfx/src/impl/fast_spheres.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_residue_view.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_residue_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/impl/trace_renderer.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gfx/src/impl/fast_spheres.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /<>/modules/gfx/src/render_options/render_options.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /<>/modules/gfx/src/render_options/line_render_options.cc [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -c /<>/modules/io/src/mol/entity_io_pqr_handler.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /<>/modules/gfx/src/render_options/custom_render_options.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/render_options/render_options.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/input.hh:30, from /<>/modules/gfx/src/render_options/render_options.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /<>/modules/gfx/src/render_options/cpk_render_options.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /<>/modules/gfx/src/render_options/simple_render_options.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/entity_io_pqr_handler.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/entity_io_pqr_handler.cc: In constructor ‘ost::io::PQRReader::PQRReader(const boost::filesystem::path&)’: /<>/modules/io/src/mol/entity_io_pqr_handler.cc:61:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 61 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/entity_io_pqr_handler.cc:28: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /<>/modules/gfx/src/render_options/sline_render_options.cc In file included from /usr/include/c++/13/bits/stl_tempbuf.h:62, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/modules/gfx/src/render_options/simple_render_options.hh:26, from /<>/modules/gfx/src/render_options/simple_render_options.cc:23: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/gfx/src/render_options/simple_render_options.cc:81:31: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /<>/modules/gfx/src/render_options/line_trace_render_options.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /<>/modules/gfx/src/render_options/cartoon_render_options.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /<>/modules/gfx/src/render_options/trace_render_options.cc [ 40%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /<>/modules/mol/base/pymod/export_surface.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /<>/modules/gfx/src/color_ops/map_handle_color_op.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /<>/modules/gfx/src/map_iso.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -c /<>/modules/io/src/mol/entity_io_mae_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, from /<>/modules/gfx/src/map_iso.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/gfx/src/map_iso.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/modules/mol/base/pymod/export_surface.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_surface.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /<>/modules/gfx/src/map_slab.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/entity_io_mae_handler.cc:38: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/entity_io_mae_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /<>/modules/gfx/src/impl/map_iso_gen.cc /<>/modules/io/src/mol/entity_io_mae_handler.cc: In constructor ‘ost::io::MAEReader::MAEReader(const boost::filesystem::path&)’: /<>/modules/io/src/mol/entity_io_mae_handler.cc:60:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 60 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/entity_io_mae_handler.cc:31: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /<>/modules/gfx/src/map_slab.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/modules/gfx/src/map_slab.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gfx/src/map_slab.cc: In function ‘std::pair ost::gfx::{anonymous}::calc_sr(float, float, float, float, float, float)’: /<>/modules/gfx/src/map_slab.cc:182:53: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 182 | float cx, float cy) | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gfx/src/impl/map_iso_gen.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /<>/modules/gfx/src/impl/map_iso_gen_s.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/gfx/src/impl/map_iso_gen_s.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /<>/modules/gfx/src/impl/map_iso_gen_s.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /<>/modules/gfx/src/impl/map_iso_gen_o.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /<>/modules/gfx/src/impl/map_octree.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, from /<>/modules/gfx/src/impl/map_iso_gen_o.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /<>/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /<>/modules/gfx/src/impl/map_octree.hh:22, from /<>/modules/gfx/src/impl/map_octree.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /<>/modules/gfx/src/impl/octree_isocont.cc /<>/modules/gfx/src/impl/map_octree.cc: In member function ‘std::pair ost::gfx::impl::MapOctree::BuildOctreeRec(const ost::gfx::impl::OcRangeVector&, uint16_t, ost::img::image_state::RealSpatialImageState*, const ost::img::Extent&, ost::gfx::impl::OctreeNode&)’: /<>/modules/gfx/src/impl/map_octree.cc:84:68: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 84 | OctreeNode& parent) | ^ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /<>/modules/io/src/mol/pdb_reader.cc [ 43%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /<>/modules/mol/base/pymod/export_bounding_box.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, from /<>/modules/gfx/src/impl/octree_isocont.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/iterator:61, from /usr/include/boost/container_hash/is_range.hpp:16, from /usr/include/boost/container_hash/hash.hpp:15, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_map.hpp:20, from /usr/include/boost/unordered_map.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Linking CXX shared library ../../../stage/lib/libost_gfx.so cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/test_texture.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/textures/test_texture.png cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/glyph_texture.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.5 -o ../../../stage/lib/libost_gfx.so.2.5.0 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o CMakeFiles/ost_gfx.dir/gfx_object.cc.o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o CMakeFiles/ost_gfx.dir/input.cc.o CMakeFiles/ost_gfx.dir/prim_list.cc.o CMakeFiles/ost_gfx.dir/scene.cc.o CMakeFiles/ost_gfx.dir/selection.cc.o CMakeFiles/ost_gfx.dir/surface.cc.o CMakeFiles/ost_gfx.dir/gradient.cc.o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o CMakeFiles/ost_gfx.dir/vertex_array.cc.o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o CMakeFiles/ost_gfx.dir/material.cc.o CMakeFiles/ost_gfx.dir/povray.cc.o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o CMakeFiles/ost_gfx.dir/texture.cc.o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/pdb_reader.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /usr/include/boost/iostreams/filter/gzip.hpp:21, from /<>/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/mol/pdb_reader.hh:28, from /<>/modules/io/src/mol/pdb_reader.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/pdb_reader.cc: In member function ‘void ost::io::PDBReader::Init(const boost::filesystem::path&)’: /<>/modules/io/src/mol/pdb_reader.cc:91:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 91 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/pdb_reader.cc:20: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/mol/pdb_reader.cc:97:49: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 97 | if(boost::iequals(boost::filesystem::extension(loc), ".pqr")) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -c /<>/modules/io/src/mol/entity_io_pdb_handler.cc cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.5.0 ../../../stage/lib/libost_gfx.so.2.5 ../../../stage/lib/libost_gfx.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 43%] Built target ost_gfx [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -c /<>/modules/io/src/mol/pdb_writer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/base/pymod/export_bounding_box.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_bounding_box.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /<>/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/io/src/mol/entity_io_pdb_handler.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/entity_io_pdb_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/io/src/mol/pdb_writer.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /<>/modules/io/src/mol/pdb_writer.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/pdb_writer.cc: In constructor ‘ost::io::PDBWriter::PDBWriter(const boost::filesystem::path&, const ost::io::IOProfile&)’: /<>/modules/io/src/mol/pdb_writer.cc:395:58: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 395 | if (boost::iequals(".pqr", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/modules/io/src/mol/pdb_writer.cc:28: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/mol/pdb_writer.cc:398:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 398 | if (boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/mol/pdb_writer.cc: In constructor ‘ost::io::PDBWriter::PDBWriter(const String&, const ost::io::IOProfile&)’: /<>/modules/io/src/mol/pdb_writer.cc:412:58: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 412 | if (boost::iequals(".pqr", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/mol/pdb_writer.cc:415:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 415 | if (boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/mol/entity_io_pdb_handler.cc: In member function ‘virtual void ost::io::EntityIOPDBHandler::Export(const ost::mol::EntityView&, const boost::filesystem::path&) const’: /<>/modules/io/src/mol/entity_io_pdb_handler.cc:52:50: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 52 | if (boost::iequals(boost::filesystem::extension(loc), ".pqr")) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/entity_io_pdb_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -c /<>/modules/io/src/mol/entity_io_sdf_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, from /<>/modules/io/src/mol/entity_io_sdf_handler.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -c /<>/modules/io/src/mol/entity_io_mmcif_handler.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /<>/modules/io/src/mol/sdf_reader.cc [ 43%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /<>/modules/mol/base/pymod/export_torsion.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /<>/modules/io/src/mol/sdf_writer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /<>/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/sdf_reader.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, from /usr/include/boost/algorithm/string.hpp:18, from /<>/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/sdf_writer.hh:35, from /<>/modules/io/src/mol/sdf_writer.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/sdf_reader.cc: In member function ‘void ost::io::SDFReader::ClearState(const boost::filesystem::path&)’: /<>/modules/io/src/mol/sdf_reader.cc:108:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 108 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/mol/sdf_reader.cc:24: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /<>/modules/io/src/mol/save_entity.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/mol/save_entity.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/src/mol/save_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /<>/modules/io/src/mol/load_entity.cc [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /<>/modules/io/src/mol/surface_io_msms_handler.cc [ 43%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /<>/modules/mol/base/pymod/export_visitor.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/load_entity.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/src/mol/load_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /<>/modules/io/src/mol/surface_io_handler.hh:25, from /<>/modules/io/src/mol/surface_io_msms_handler.hh:22, from /<>/modules/io/src/mol/surface_io_msms_handler.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/modules/io/src/mol/surface_io_msms_handler.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/mol/load_entity.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/mol/surface_io_msms_handler.cc: In function ‘std::pair ost::io::{anonymous}::detect_files(const boost::filesystem::path&)’: /<>/modules/io/src/mol/surface_io_msms_handler.cc:36:45: warning: ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’ is deprecated: Use path::replace_extension() instead [-Wdeprecated-declarations] 36 | return std::make_pair(bf::change_extension(loc, ".vert"), | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /<>/modules/io/src/mol/surface_io_msms_handler.cc:25: /usr/include/boost/filesystem/convenience.hpp:41:13: note: declared here 41 | inline path change_extension(const path& p, const path& new_extension) | ^~~~~~~~~~~~~~~~ /<>/modules/io/src/mol/surface_io_msms_handler.cc:37:45: warning: ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’ is deprecated: Use path::replace_extension() instead [-Wdeprecated-declarations] 37 | bf::change_extension(loc, ".face")); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:41:13: note: declared here 41 | inline path change_extension(const path& p, const path& new_extension) | ^~~~~~~~~~~~~~~~ [ 43%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /<>/modules/io/src/mol/load_surface.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /<>/modules/io/src/mol/chemdict_parser.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/pymod/export_visitor.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_visitor.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/modules/io/src/mol/load_surface.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/src/mol/load_surface.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/mol/load_surface.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /<>/modules/io/src/mol/chemdict_parser.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /<>/modules/mol/base/pymod/wrap_mol.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /<>/modules/io/src/mol/io_profile.cc [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /<>/modules/io/src/mol/dcd_io.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/modules/io/src/mol/io_profile.hh:24, from /<>/modules/io/src/mol/io_profile.cc:1: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/mol/io_profile.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /<>/modules/io/src/mol/star_parser.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/src/mol/dcd_io.cc:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/io/src/mol/dcd_io.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/mol/pdb_reader.hh:28, from /<>/modules/io/src/mol/dcd_io.cc:40: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, from /<>/modules/mol/base/pymod/wrap_mol.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /<>/modules/io/src/mol/mmcif_reader.cc [ 45%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /<>/modules/mol/base/pymod/export_entity_property_mapper.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/io/src/mol/mmcif_reader.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/profile.hh:22, from /<>/modules/io/src/mol/mmcif_reader.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /<>/modules/io/src/mol/mmcif_reader.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /<>/modules/io/src/mol/mmcif_info.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /<>/modules/io/src/mol/mmcif_info.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_exception.hh:22, from /<>/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /<>/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /<>/modules/io/src/mol/pdb_str.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh:23, from /<>/modules/io/src/mol/pdb_str.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/io/src/mol/pdb_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/io/src/mol/pdb_str.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/base/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 45%] Built target _ost_mol make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 45%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /<>/modules/seq/base/pymod/export_sequence.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_str.cc.o -c /<>/modules/io/src/mol/sdf_str.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o -c /<>/modules/io/src/mol/mmcif_str.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh:23, from /<>/modules/io/src/mol/sdf_str.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/io/src/mol/sdf_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh:24, from /<>/modules/io/src/mol/mmcif_str.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/io/src/mol/mmcif_str.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mmcif_reader.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/seq/base/pymod/export_sequence.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/seq/base/pymod/export_sequence.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/modules/seq/base/pymod/export_sequence.cc:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /<>/modules/io/src/mol/stereochemical_params_reader.cc [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /<>/modules/io/src/mol/omf.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /<>/modules/io/src/mol/stereochemical_params_reader.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/locale:41, from /usr/include/boost/filesystem/detail/path_traits.hpp:18, from /usr/include/boost/filesystem/path.hpp:21, from /usr/include/boost/filesystem/fstream.hpp:17, from /<>/modules/io/src/mol/stereochemical_params_reader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/modules/io/src/mol/omf.cc:2: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /<>/modules/io/src/mol/omf.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /<>/modules/io/src/mol/omf.hh:29, from /<>/modules/io/src/mol/omf.cc:6: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /<>/modules/io/src/seq/clustal_io_handler.cc /<>/modules/io/src/mol/omf.cc: In function ‘void {anonymous}::DumpName(std::ostream&, const String&)’: /<>/modules/io/src/mol/omf.cc:816:43: warning: the address of ‘static constexpr unsigned char std::numeric_limits::max()’ will never be NULL [-Waddress] 816 | ss << std::numeric_limits::max << ". "; | ^~~ In file included from /usr/include/c++/13/bits/specfun.h:44: /usr/include/c++/13/limits:598:7: note: ‘static constexpr unsigned char std::numeric_limits::max()’ declared here 598 | max() _GLIBCXX_USE_NOEXCEPT { return __SCHAR_MAX__ * 2U + 1; } | ^~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /<>/modules/io/src/seq/load.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/seq/load.hh:27, from /<>/modules/io/src/seq/load.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /<>/modules/io/src/seq/load.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/modules/io/src/seq/clustal_io_handler.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/modules/io/src/seq/clustal_io_handler.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/seq/sequence_io_handler.hh:27, from /<>/modules/io/src/seq/clustal_io_handler.hh:25, from /<>/modules/io/src/seq/clustal_io_handler.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o -MF CMakeFiles/ost_io.dir/seq/save.cc.o.d -o CMakeFiles/ost_io.dir/seq/save.cc.o -c /<>/modules/io/src/seq/save.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -c /<>/modules/io/src/seq/fasta_io_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/seq/save.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/io/src/seq/save.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/seq/sequence_io_handler.hh:27, from /<>/modules/io/src/seq/fasta_io_handler.hh:25, from /<>/modules/io/src/seq/fasta_io_handler.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /<>/modules/io/src/seq/fasta_io_handler.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /<>/modules/io/src/seq/pir_io_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/io/src/seq/sequence_io_handler.hh:27, from /<>/modules/io/src/seq/pir_io_handler.hh:25, from /<>/modules/io/src/seq/pir_io_handler.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /<>/modules/io/src/seq/pir_io_handler.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /<>/modules/io/src/seq/promod_io_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/modules/io/src/seq/promod_io_handler.hh:26, from /<>/modules/io/src/seq/promod_io_handler.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /<>/modules/io/src/seq/hhm_io_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /<>/modules/io/src/seq/pssm_io_handler.cc /<>/modules/io/src/seq/hhm_io_handler.cc: In member function ‘virtual void ost::io::HhmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)’: /<>/modules/io/src/seq/hhm_io_handler.cc:133:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 133 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/seq/hhm_io_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ /<>/modules/io/src/seq/pssm_io_handler.cc: In member function ‘virtual void ost::io::PssmIOHandler::Import(ost::seq::ProfileHandle&, const boost::filesystem::path&)’: /<>/modules/io/src/seq/pssm_io_handler.cc:47:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 47 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/seq/pssm_io_handler.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /<>/modules/io/src/img/load_map.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /<>/modules/io/src/img/map_io_dx_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/modules/io/src/img/load_map.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/src/img/load_map.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/src/img/load_map.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /<>/modules/seq/base/pymod/export_profile_handle.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /<>/modules/io/src/img/map_io_dx_handler.cc:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/modules/io/src/img/map_io_dx_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/io/src/img/map_io_dx_handler.cc: In member function ‘virtual void ost::io::MapIODxHandler::Import(ost::img::MapHandle&, const boost::filesystem::path&, const ost::io::ImageFormatBase&)’: /<>/modules/io/src/img/map_io_dx_handler.cc:97:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 97 | if (boost::iequals(".gz", boost::filesystem::extension(loc))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/modules/io/src/img/map_io_dx_handler.cc:31: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /<>/modules/io/src/img/map_io_spi_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -c /<>/modules/io/src/img/map_io_situs_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /<>/modules/io/src/img/map_io_spi_handler.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/io/src/img/map_io_spi_handler.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /<>/modules/io/src/img/map_io_situs_handler.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /<>/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /<>/modules/io/src/img/map_io_mrc_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /<>/modules/io/src/img/map_io_dm3_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /<>/modules/io/src/img/map_io_tiff_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/io/src/img/map_io_dm3_handler.cc:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/io/src/img/map_io_tiff_handler.cc:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/io/src/img/map_io_tiff_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/io/src/img/map_io_mrc_handler.cc:76: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/img/map_io_mrc_handler.cc:58: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /<>/modules/seq/base/pymod/wrap_seq.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /<>/modules/io/src/img/map_io_dat_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /<>/modules/io/src/img/map_io_ipl_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/io/src/img/map_io_dat_handler.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/shared_array.hpp:21, from /usr/include/boost/shared_array.hpp:17, from /<>/modules/io/src/img/map_io_dat_handler.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/io/src/img/map_io_ipl_handler.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /<>/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/seq/base/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 48%] Built target _ost_seq make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/pymod /<>/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 48%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /<>/modules/bindings/pymod/export_tmalign.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /<>/modules/io/src/img/map_io_jpk_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /<>/modules/io/src/img/map_io_nanoscope_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, from /<>/modules/io/src/img/map_io_jpk_handler.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /<>/modules/io/src/img/map_io_jpk_handler.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /<>/modules/io/src/img/map_io_png_handler.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /<>/modules/bindings/pymod/export_tmalign.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/bindings/pymod/export_tmalign.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/modules/io/src/img/map_io_nanoscope_handler.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/modules/io/src/img/map_io_nanoscope_handler.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/modules/io/src/img/map_io_png_handler.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/io/src/img/map_io_png_handler.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /<>/modules/io/src/img/map_io_df3_handler.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /<>/modules/io/src/img/image_format.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o -MF CMakeFiles/ost_io.dir/img/tiff_util.cc.o.d -o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -c /<>/modules/io/src/img/tiff_util.cc [ 49%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -MF CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o.d -o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -c /<>/modules/bindings/pymod/wrap_bindings.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /<>/modules/io/src/img/map_io_df3_handler.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /<>/modules/io/src/img/map_io_df3_handler.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/pymod /<>/obj-aarch64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 49%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /<>/modules/db/pymod/export_linear_db.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /<>/modules/io/src/img/tiff_util.hh:27, from /<>/modules/io/src/img/tiff_util.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/complex:44, from /<>/modules/io/src/img/tiff_util.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o cd /<>/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /<>/modules/db/pymod/wrap_db.cc [ 49%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/bindings/_ost_bindings.so CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_bindings.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/lga.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/hbplus.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/msms.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/tmtools.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/dssp.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/clustalw.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/utils.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/naccess.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/hhblits.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/hhblits2.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/hhblits3.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/blast.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/cadscore.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/kclust.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/ialign.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/mmseqs2.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/bindings/pymod/dockq.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/bindings/./dockq.pyc\",\"dockq.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 49%] Built target _ost_bindings make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 49%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /<>/modules/seq/alg/pymod/wrap_seq_alg.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /<>/modules/db/pymod/export_linear_db.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/db/pymod/export_linear_db.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /<>/modules/seq/alg/pymod/wrap_seq_alg.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/seq/alg/pymod/wrap_seq_alg.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/ins_del.hh:25, from /<>/modules/seq/alg/pymod/wrap_seq_alg.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_io.so.2.5 -o ../../../stage/lib/libost_io.so.2.5.0 CMakeFiles/ost_io.dir/io_manager.cc.o CMakeFiles/ost_io.dir/convert.cc.o CMakeFiles/ost_io.dir/io_utils.cc.o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o CMakeFiles/ost_io.dir/mol/save_entity.cc.o CMakeFiles/ost_io.dir/mol/load_entity.cc.o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o CMakeFiles/ost_io.dir/mol/load_surface.cc.o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o CMakeFiles/ost_io.dir/mol/io_profile.cc.o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o CMakeFiles/ost_io.dir/mol/star_parser.cc.o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o CMakeFiles/ost_io.dir/mol/sdf_str.cc.o CMakeFiles/ost_io.dir/mol/mmcif_str.cc.o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o CMakeFiles/ost_io.dir/mol/omf.cc.o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o CMakeFiles/ost_io.dir/seq/load.cc.o CMakeFiles/ost_io.dir/seq/save.cc.o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o CMakeFiles/ost_io.dir/img/load_map.cc.o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o CMakeFiles/ost_io.dir/img/image_format.cc.o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_io.so.2.5.0 ../../../stage/lib/libost_io.so.2.5 ../../../stage/lib/libost_io.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 49%] Built target ost_io make -f modules/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/depend make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/src /<>/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/chemdict_tool.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/build [ 49%] Generating tools/moc_tool_options_win.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 49%] Building CXX object modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -MF CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o.d -o CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -c /<>/modules/conop/src/chemdict_tool.cc [ 49%] Generating data_viewer/moc_argand.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters [ 49%] Generating data_viewer/moc_data_viewer.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters [ 49%] Generating data_viewer/moc_data_viewer_panel_base.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters [ 49%] Generating data_viewer/moc_fft_panel.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters [ 49%] Generating data_viewer/moc_info_panel.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters [ 49%] Generating data_viewer/moc_null_overlay.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp_parameters [ 50%] Generating data_viewer/moc_overlay_base.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp_parameters [ 50%] Generating data_viewer/moc_overlay_manager_gui.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp_parameters [ 50%] Generating data_viewer/moc_pointlist_overlay_base.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp_parameters [ 50%] Generating messages/moc_log_reader.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp_parameters [ 50%] Generating messages/moc_message_box_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp_parameters [ 50%] Generating messages/moc_message_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp_parameters [ 50%] Generating moc_dock_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_dock_widget.cpp_parameters [ 50%] Generating moc_file_browser.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp_parameters [ 50%] Generating moc_file_type_dialog.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp_parameters [ 50%] Generating moc_file_viewer.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_viewer.cpp_parameters [ 50%] Generating moc_gl_canvas.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp_parameters [ 50%] Generating moc_gl_win.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_win.cpp_parameters [ 50%] Generating moc_gosty_app.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty_app.cpp_parameters [ 50%] Generating moc_main.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main.cpp_parameters [ 50%] Generating moc_main_area.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main_area.cpp_parameters [ 50%] Generating moc_main_window.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main_window.cpp_parameters [ 51%] Generating moc_perspective.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_perspective.cpp_parameters [ 51%] Generating moc_scene_menu.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_menu.cpp_parameters [ 51%] Generating moc_scene_selection.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters [ 51%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so cd /<>/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_db.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/db/_ost_db.so CMakeFiles/_ost_db.dir/export_linear_db.cc.o CMakeFiles/_ost_db.dir/wrap_db.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 cd /<>/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/db/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 51%] Built target _ost_db make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/tests /<>/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 51%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -MF CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o.d -o CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -c /<>/modules/io/tests/test_mae_standalone.cc [ 51%] Generating moc_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget.cpp_parameters [ 51%] Generating moc_widget_geom_handler.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters [ 51%] Generating moc_widget_pool.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters [ 51%] Generating panels/moc_bottom_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters [ 51%] Generating panels/moc_button_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters [ 51%] Generating panels/moc_button_box.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters [ 51%] Generating panels/moc_drop_box.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters [ 51%] Generating panels/moc_event_button.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters [ 51%] Generating panels/moc_panel_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp_parameters [ 53%] Generating panels/moc_panel_bar_widget_holder.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp_parameters [ 53%] Generating panels/moc_panel_manager.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters [ 53%] Generating panels/moc_panel_widget_container.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters [ 53%] Generating panels/moc_side_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters [ 53%] Generating panels/moc_splitter_panel_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters [ 53%] Generating panels/moc_tabbed_panel_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters [ 53%] Generating python_shell/moc_completer_base.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters [ 54%] Generating python_shell/moc_gutter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp_parameters [ 54%] Generating python_shell/moc_main_thread_runner.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters [ 54%] Generating python_shell/moc_output_redirector.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters [ 54%] Generating python_shell/moc_path_completer.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters [ 54%] Generating python_shell/moc_python_completer.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters [ 54%] Generating python_shell/moc_python_interpreter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters [ 54%] Generating python_shell/moc_python_interpreter_worker.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp_parameters [ 54%] Generating python_shell/moc_python_namespace_tree_model.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters [ 54%] Generating python_shell/moc_python_shell.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters [ 54%] Generating python_shell/moc_python_shell_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters [ 55%] Generating python_shell/moc_state.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters [ 55%] Generating python_shell/moc_state_machine.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters [ 55%] Generating python_shell/moc_text_logger.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters [ 55%] Generating python_shell/moc_transition.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters [ 55%] Generating python_shell/moc_transition_guard.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp_parameters [ 55%] Generating scene_win/moc_context_menu.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp_parameters In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /<>/modules/conop/src/chemdict_tool.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/conop/src/chemdict_tool.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/conop/src/chemdict_tool.cc: In function ‘int main(int, const char**)’: /<>/modules/conop/src/chemdict_tool.cc:69:57: warning: ‘std::string boost::filesystem::extension(const path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 69 | if (boost::iequals(".gz", boost::filesystem::extension(argv[2]))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ In file included from /<>/modules/conop/src/chemdict_tool.cc:27: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ [ 55%] Generating scene_win/moc_current_selection_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters [ 55%] Generating scene_win/moc_custom_part_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp_parameters In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/io/tests/test_mae_standalone.cc:2: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/io/tests/test_mae_standalone.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Generating scene_win/moc_entity_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters [ 55%] Generating scene_win/moc_entity_part_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters [ 55%] Generating scene_win/moc_gfx_scene_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters [ 55%] Generating scene_win/moc_label_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters [ 56%] Generating scene_win/moc_render_mode_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters [ 56%] Linking CXX executable ../../../stage/bin/test_mae_standalone cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 56%] Built target test_mae_standalone make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/src /<>/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/lddt.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/build [ 56%] Generating scene_win/moc_render_modes_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 56%] Building CXX object modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /<>/modules/mol/alg/src/lddt.cc [ 56%] Linking CXX executable ../../../stage/bin/chemdict_tool cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 56%] Generating scene_win/moc_root_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters [ 56%] Generating scene_win/moc_scene_node.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters [ 56%] Generating scene_win/moc_scene_win.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 56%] Built target chemdict_tool make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/src /<>/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 56%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -MF CMakeFiles/ost_mol_mm.dir/forcefield.cc.o.d -o CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -c /<>/modules/mol/mm/src/forcefield.cc [ 56%] Generating scene_win/moc_scene_win_model.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters [ 56%] Generating sequence_viewer/moc_align_properties_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters [ 56%] Generating sequence_viewer/moc_alignment_view_object.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters [ 58%] Generating sequence_viewer/moc_background_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/mol/alg/src/lddt.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /<>/modules/mol/alg/src/lddt.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /<>/modules/mol/alg/src/lddt.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /<>/modules/mol/mm/src/forcefield.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/modules/mol/alg/src/lddt.cc:39: /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh: At global scope: /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters /<>/modules/mol/alg/src/lddt.cc: In function ‘ost::conop::CompoundLibPtr load_compound_lib(const String&)’: /<>/modules/mol/alg/src/lddt.cc:138:48: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 138 | fs::path path_only=path_and_exe.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/boost/filesystem/fstream.hpp:17, from /<>/modules/mol/alg/src/lddt.cc:26: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ /<>/modules/mol/alg/src/lddt.cc:139:48: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 139 | fs::path share_path = path_only.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~^~ /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ [ 58%] Generating sequence_viewer/moc_base_view_object.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters [ 58%] Generating sequence_viewer/moc_conservation_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters [ 58%] Generating sequence_viewer/moc_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters [ 58%] Generating sequence_viewer/moc_secstr_row.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters [ 58%] Generating sequence_viewer/moc_seq_secstr_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp_parameters [ 58%] Generating sequence_viewer/moc_seq_selection_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp_parameters [ 58%] Generating sequence_viewer/moc_seq_text_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp_parameters [ 58%] Generating sequence_viewer/moc_sequence_delegate.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp_parameters [ 58%] Generating sequence_viewer/moc_sequence_model.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp_parameters [ 58%] Generating sequence_viewer/moc_sequence_row.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp_parameters [ 58%] Linking CXX executable ../../../../stage/bin/lddt cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 59%] Generating sequence_viewer/moc_sequence_search_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp_parameters make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 59%] Built target lddt make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/molck /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/tools/molck /<>/obj-aarch64-linux-gnu/tools/molck/CMakeFiles/molck.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 60%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o cd /<>/obj-aarch64-linux-gnu/tools/molck && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT tools/molck/CMakeFiles/molck.dir/main.cc.o -MF CMakeFiles/molck.dir/main.cc.o.d -o CMakeFiles/molck.dir/main.cc.o -c /<>/tools/molck/main.cc [ 60%] Generating sequence_viewer/moc_sequence_table_view.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp_parameters [ 60%] Generating sequence_viewer/moc_sequence_view_object.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp_parameters [ 60%] Generating sequence_viewer/moc_sequence_viewer.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp_parameters [ 60%] Generating sequence_viewer/moc_tick_painter.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp_parameters [ 60%] Generating sequence_viewer/moc_title_row.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp_parameters [ 60%] Generating tools/moc_measure_tool.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp_parameters [ 60%] Generating tools/moc_tool.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool.cpp_parameters [ 60%] Generating tools/moc_tool_bar.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp_parameters [ 62%] Generating tools/moc_tool_manager.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp_parameters [ 62%] Generating tools/moc_tool_option.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp_parameters [ 62%] Generating tools/moc_tool_option_group.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp_parameters [ 62%] Generating tools/moc_tool_options.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp_parameters [ 62%] Generating tools/moc_tool_options_widget.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp_parameters cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/src /<>/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 62%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/tools/molck/main.cc:8: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /<>/tools/molck/main.cc:2: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/tools/molck/main.cc:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/tools/molck/main.cc: In function ‘ost::conop::CompoundLibPtr load_compound_lib(const String&)’: /<>/tools/molck/main.cc:119:48: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 119 | fs::path path_only=path_and_exe.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /<>/tools/molck/main.cc:3: /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ /<>/tools/molck/main.cc:120:48: warning: ‘boost::filesystem::path boost::filesystem::path::branch_path() const’ is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 120 | fs::path share_path = path_only.branch_path(); | ~~~~~~~~~~~~~~~~~~~~~^~ /usr/include/boost/filesystem/path.hpp:1129:10: note: declared here 1129 | path branch_path() const { return parent_path(); } | ^~~~~~~~~~~ [ 63%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/seq/alg/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/seq/alg/pymod/mat.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/seq/alg/pymod/renumber.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/seq/alg/pymod/aaindex.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 63%] Built target _ost_seq_alg make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/pymod /<>/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 63%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -MF CMakeFiles/_ost_conop.dir/wrap_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -c /<>/modules/conop/pymod/wrap_conop.cc [ 63%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -MF CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o.d -o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -c /<>/modules/mol/mm/src/ff_reader.cc [ 63%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /<>/modules/mol/mm/src/ff_reader.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 63%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /<>/modules/conop/pymod/export_compound.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 63%] Linking CXX executable ../../stage/bin/molck cd /<>/obj-aarch64-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.5.0 ../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../stage/lib/libost_seq_alg.so.2.5.0 ../../stage/lib/libost_conop.so.2.5.0 ../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.5.0 ../../stage/lib/libost_mol.so.2.5.0 ../../stage/lib/libost_img_alg.so.2.5.0 ../../stage/lib/libost_img.so.2.5.0 ../../stage/lib/libost_info.so.2.5.0 ../../stage/lib/libost_base.so.2.5.0 ../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 63%] Built target molck [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /<>/modules/conop/pymod/export_processor.cc [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_file_viewer.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /<>/modules/conop/pymod/export_compound.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_compound.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/processor.hh:22, from /<>/modules/conop/pymod/export_processor.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_processor.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_win.cpp [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_menu.cpp [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /<>/modules/conop/pymod/export_heuristic.cc [ 64%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -MF CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o.d -o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -c /<>/modules/mol/mm/src/buildingblock.cc [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty_app.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/heuristic.hh:22, from /<>/modules/conop/pymod/export_heuristic.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_heuristic.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/modules/mol/mm/src/buildingblock.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /<>/modules/conop/pymod/export_amino_acids.cc [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /<>/modules/conop/pymod/export_conop.cc [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /<>/modules/conop/pymod/export_amino_acids.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_amino_acids.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /<>/modules/conop/pymod/export_conop.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_conop.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /<>/modules/mol/mm/src/gromacs_block_modifiers.cc [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /<>/modules/conop/pymod/export_diag.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:28, from /<>/modules/mol/mm/src/gromacs_block_modifiers.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main.cpp:10: /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of ‘ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]’: /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of ‘ost::gui::WidgetStateSaver::’ will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: ‘ost::gui::WidgetStateSaver::’ declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main_area.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/diag.hh:23, from /<>/modules/conop/pymod/export_diag.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_diag.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /<>/modules/conop/pymod/export_rule_based.cc [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_perspective.cpp [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_dock_widget.cpp [ 65%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /<>/modules/conop/pymod/export_ring_finder.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -c /<>/modules/mol/mm/src/heuristic_block_modifiers.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, from /<>/modules/conop/pymod/export_rule_based.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_rule_based.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_main_window.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:28, from /<>/modules/mol/mm/src/heuristic_block_modifiers.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/ring_finder.hh:27, from /<>/modules/conop/pymod/export_ring_finder.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/conop/pymod/export_ring_finder.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o -MF CMakeFiles/ost_mol_mm.dir/interaction.cc.o.d -o CMakeFiles/ost_mol_mm.dir/interaction.cc.o -c /<>/modules/mol/mm/src/interaction.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -MF CMakeFiles/ost_mol_mm.dir/simulation.cc.o.d -o CMakeFiles/ost_mol_mm.dir/simulation.cc.o -c /<>/modules/mol/mm/src/simulation.cc [ 65%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/conop/_ost_conop.so cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/conop/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/conop/pymod/cleanup.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 65%] Built target _ost_conop make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/pymod /<>/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 65%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /<>/modules/gfx/pymod/wrap_gfx.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/modules/mol/mm/src/interaction.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /<>/modules/mol/mm/src/simulation.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o -MF CMakeFiles/ost_mol_mm.dir/modeller.cc.o.d -o CMakeFiles/ost_mol_mm.dir/modeller.cc.o -c /<>/modules/mol/mm/src/modeller.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/modules/mol/mm/src/modeller.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /<>/modules/gfx/pymod/wrap_gfx.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/wrap_gfx.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_pool.cpp [ 65%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /<>/modules/gfx/pymod/export_scene.cc [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -MF CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o.d -o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -c /<>/modules/mol/mm/src/state_extractor.cc [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -MF CMakeFiles/ost_mol_mm.dir/observer.cc.o.d -o CMakeFiles/ost_mol_mm.dir/observer.cc.o -c /<>/modules/mol/mm/src/observer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gfx/pymod/export_scene.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_scene.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /<>/modules/mol/mm/src/observer.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /<>/modules/mol/mm/src/system_creator.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:28, from /<>/modules/mol/mm/src/system_creator.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /<>/modules/mol/mm/src/topology_creator.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /<>/modules/gfx/pymod/export_gfx_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:29, from /<>/modules/mol/mm/src/topology_creator.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp [ 68%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /<>/modules/mol/mm/src/topology.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /<>/modules/mol/mm/src/topology.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /<>/modules/gfx/pymod/export_symmetry_node.cc [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp [ 68%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /<>/modules/mol/mm/src/steep.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, from /<>/modules/gfx/pymod/export_symmetry_node.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_symmetry_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/AMBER03.dat /<>/obj-aarch64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/CHARMM27.dat /<>/obj-aarch64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -Wl,-soname,libost_mol_mm.so.2.5 -o ../../../../stage/lib/libost_mol_mm.so.2.5.0 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.5.0 /usr/lib/aarch64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.5.0 ../../../../stage/lib/libost_mol_mm.so.2.5 ../../../../stage/lib/libost_mol_mm.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 68%] Built target ost_mol_mm make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 68%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /<>/modules/mol/alg/pymod/wrap_mol_alg.cc [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp [ 68%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /<>/modules/gfx/pymod/export_gfx_obj.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /<>/modules/mol/alg/pymod/wrap_mol_alg.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/wrap_mol_alg.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gfx/pymod/export_gfx_obj.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_gfx_obj.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /<>/modules/gfx/pymod/export_entity.cc [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gfx/pymod/export_entity.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /<>/modules/mol/alg/pymod/export_svd_superpose.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp [ 70%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /<>/modules/gfx/pymod/export_surface.cc [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /<>/modules/mol/alg/pymod/export_svd_superpose.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_svd_superpose.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/surface.hh:31, from /<>/modules/gfx/pymod/export_surface.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_surface.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64: /usr/include/c++/13/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float]’: /<>/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp [ 72%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /<>/modules/mol/alg/pymod/export_clash.cc [ 72%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /<>/modules/gfx/pymod/export_primitives.cc [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, from /<>/modules/mol/alg/pymod/export_clash.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_clash.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp [ 72%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /<>/modules/mol/alg/pymod/export_trajectory_analysis.cc [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /<>/modules/gfx/pymod/export_primitives.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_primitives.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /<>/modules/gfx/pymod/export_primlist.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, from /<>/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, from /<>/modules/gfx/pymod/export_primlist.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_primlist.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /<>/modules/mol/alg/pymod/export_structure_analysis.cc [ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /<>/modules/gfx/pymod/export_scene_observer.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, from /<>/modules/mol/alg/pymod/export_structure_analysis.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_structure_analysis.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, from /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /<>/modules/gfx/pymod/export_render_options.cc [ 73%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /<>/modules/mol/alg/pymod/export_contact_overlap.cc [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, from /<>/modules/mol/alg/pymod/export_contact_overlap.cc:4: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_contact_overlap.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp [ 74%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /<>/modules/gfx/pymod/export_color.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/modules/gfx/pymod/export_color.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_color.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/custom_part_node.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp [ 74%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /<>/modules/mol/alg/pymod/export_accessibility.cc [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp [ 74%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /<>/modules/gfx/pymod/export_gradient.cc [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /<>/modules/mol/alg/pymod/export_accessibility.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_accessibility.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gradient.hh:28, from /<>/modules/gfx/pymod/export_gradient.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_gradient.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /<>/modules/mol/alg/pymod/export_sec_structure.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp [ 75%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /<>/modules/gfx/pymod/export_color_ops.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /<>/modules/mol/alg/pymod/export_sec_structure.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_sec_structure.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win_model.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /<>/modules/gfx/pymod/export_color_ops.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_color_ops.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp [ 75%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /<>/modules/mol/alg/pymod/export_non_standard.cc [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/pymod/export_non_standard.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_non_standard.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /<>/modules/mol/alg/pymod/export_molck.cc [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28, from /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/argand.hh:30, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data_observer.hh:31, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, from /<>/modules/mol/alg/pymod/export_molck.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/modules/mol/alg/pymod/export_molck.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/info_panel.hh:30, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp [ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /<>/modules/gfx/pymod/export_glwin_base.cc [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /<>/modules/mol/alg/pymod/export_membrane.cc [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /<>/modules/gfx/pymod/export_exporter.cc [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /<>/modules/mol/alg/pymod/export_membrane.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_membrane.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/pointlist_overlay_base.hh:31, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:10: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /<>/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:9: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /<>/modules/gui/src/thin_splitter.cc [ 79%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /<>/modules/mol/alg/pymod/export_entity_to_density.cc [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /<>/modules/gui/src/perspective.cc [ 81%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /<>/modules/gfx/pymod/export_bitmap.cc [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o -MF CMakeFiles/ost_gui.dir/widget_registry.cc.o.d -o CMakeFiles/ost_gui.dir/widget_registry.cc.o -c /<>/modules/gui/src/widget_registry.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, from /<>/modules/gui/src/perspective.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/platform.hh:22, from /<>/modules/gui/src/perspective.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, from /<>/modules/mol/alg/pymod/export_entity_to_density.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/alg/pymod/export_entity_to_density.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /<>/modules/gui/src/file_browser.cc [ 81%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /<>/modules/gui/src/file_type_dialog.cc [ 81%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /<>/modules/gfx/pymod/export_map.cc cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/views.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/superpose.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/qsscoring.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/trajectory_analysis.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" trajectory_analysis.py:59: SyntaxWarning: invalid escape sequence '\ ' trajectory_analysis.py:98: SyntaxWarning: invalid escape sequence '\ ' trajectory_analysis.py:141: SyntaxWarning: invalid escape sequence '\ ' trajectory_analysis.py:174: SyntaxWarning: invalid escape sequence '\ ' trajectory_analysis.py:233: SyntaxWarning: invalid escape sequence '\ ' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/structure_analysis.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" structure_analysis.py:65: SyntaxWarning: invalid escape sequence '\ ' structure_analysis.py:157: SyntaxWarning: invalid escape sequence '\ ' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/helix_kinks.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/hbond.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/lddt.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./lddt.pyc\",\"lddt.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/qsscore.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./qsscore.pyc\",\"qsscore.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/scoring.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./scoring.pyc\",\"scoring.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/chain_mapping.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./chain_mapping.pyc\",\"chain_mapping.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/stereochemistry.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./stereochemistry.pyc\",\"stereochemistry.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/ligand_scoring.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./ligand_scoring.pyc\",\"ligand_scoring.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/alg/pymod/dockq.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/alg/./dockq.pyc\",\"dockq.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 81%] Built target _ost_mol_alg make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/pymod /<>/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 81%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /<>/modules/io/pymod/wrap_io.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/modules/gui/src/file_type_dialog.hh:31, from /<>/modules/gui/src/file_type_dialog.cc:19: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/file_type_dialog.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, from /<>/modules/gfx/pymod/export_map.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gfx/pymod/export_map.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gui/src/file_browser.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/file_browser.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/pymod/wrap_io.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/io/pymod/wrap_io.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, from /<>/modules/gui/src/file_browser.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gui/src/file_browser.cc: In constructor ‘ost::gui::FileBrowser::FileBrowser(QWidget*)’: /<>/modules/gui/src/file_browser.cc:62:13: warning: ‘QDirModel::QDirModel(QObject*)’ is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 62 | model_(new QDirModel), | ^~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /<>/modules/gui/src/file_browser.cc:53: /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ /<>/modules/gui/src/file_browser.cc: In constructor ‘ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)’: /<>/modules/gui/src/file_browser.cc:102:13: warning: ‘QDirModel::QDirModel(QObject*)’ is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 102 | model_(new QDirModel), | ^~~~~~~~~ /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /<>/modules/gui/src/file_viewer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /<>/modules/io/pymod/wrap_io.cc:37: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /<>/modules/gui/src/main.cc [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /<>/modules/gui/src/gl_canvas.cc [ 81%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/pymod/gradients.xml /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/gradients.xml cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gfx/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gfx/pymod/py_gfx_obj.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 81%] Built target _ost_gfx [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /<>/modules/gui/src/dock_widget.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /<>/modules/gui/src/main_window.cc [ 82%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /<>/modules/io/pymod/export_pdb_io.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /<>/modules/gui/src/main.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/main.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of ‘ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]’: /<>/modules/gui/src/main.cc:70:69: required from here /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:323:8: warning: the address of ‘ost::gui::WidgetStateSaver::’ will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: ‘ost::gui::WidgetStateSaver::’ declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of ‘void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]’: /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:286:5: required from ‘ost::gui::WidgetStateSaver::WidgetStateSaver(const QString&, QPoint, QSize, QWidget*) [with BASE = QMainWindow]’ /<>/modules/gui/src/main.cc:70:69: required from here /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:305:10: warning: the address of ‘ost::gui::WidgetStateSaver::’ will never be NULL [-Waddress] 305 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: ‘ost::gui::WidgetStateSaver::’ declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/gl_canvas.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, from /<>/modules/gui/src/gl_canvas.hh:22, from /<>/modules/gui/src/gl_canvas.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /<>/modules/gui/src/gl_win.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /<>/modules/gui/src/scene_menu.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -MF CMakeFiles/ost_gui.dir/widget.cc.o.d -o CMakeFiles/ost_gui.dir/widget.cc.o -c /<>/modules/gui/src/widget.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /<>/modules/io/pymod/export_pdb_io.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/io/pymod/export_pdb_io.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/io/pymod/export_pdb_io.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /<>/modules/gui/src/admin.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /<>/modules/gui/src/widget_pool.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/gl_win.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/gl_win.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /<>/modules/gui/src/scene_menu.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_menu.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/scene_menu.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /<>/modules/gui/src/messages/message_widget.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /<>/modules/gui/src/messages/message_box_widget.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /<>/modules/gui/src/messages/log_reader.cc [ 82%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /<>/modules/io/pymod/export_mmcif_io.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/align_properties_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /<>/modules/gui/src/sequence_viewer/base_row.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /<>/modules/io/pymod/export_mmcif_io.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/io/pymod/export_mmcif_io.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /<>/modules/io/pymod/export_mmcif_io.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/background_painter.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/modules/gui/src/sequence_viewer/base_row.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/background_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/background_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/conservation_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /<>/modules/gui/src/sequence_viewer/secstr_row.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/seq_secstr_painter.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gui/src/sequence_viewer/secstr_row.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/sequence_viewer/secstr_row.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_secstr_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/seq_selection_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/seq_text_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_delegate.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_model.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_row.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/modules/gui/src/sequence_viewer/title_row.hh:27, from /<>/modules/gui/src/sequence_viewer/sequence_model.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_search_bar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /<>/modules/gui/src/sequence_viewer/sequence_model.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gui/src/sequence_viewer/sequence_row.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /<>/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/sequence_viewer/sequence_row.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /<>/modules/gui/src/sequence_viewer/sequence_row.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_table_view.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /<>/modules/gui/src/sequence_viewer/sequence_table_view.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/sequence_viewer/sequence_table_view.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_viewer.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /<>/modules/gui/src/sequence_viewer/tick_painter.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /<>/modules/gui/src/sequence_viewer/title_row.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /<>/modules/gui/src/sequence_viewer/title_row.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /<>/modules/gui/src/sequence_viewer/sequence_viewer.cc:39: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_model.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/tick_painter.hh:27, from /<>/modules/gui/src/sequence_viewer/tick_painter.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qglobal.h:142, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:4, from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGuiDepends:3, from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGui:3, from /<>/modules/gui/src/sequence_viewer/tick_painter.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /<>/modules/gui/src/sequence_viewer/alignment_view_object.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /<>/modules/gui/src/sequence_viewer/base_view_object.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /<>/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -c /<>/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /<>/modules/gui/src/sequence_viewer/painter.hh:27, from /<>/modules/gui/src/sequence_viewer/base_row.hh:27, from /<>/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /<>/modules/gui/src/sequence_viewer/base_view_object.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh:30, from /<>/modules/gui/src/sequence_viewer/alignment_view_object.hh:32, from /<>/modules/gui/src/sequence_viewer/alignment_view_object.cc:41: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh:30, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gosty_app.cc.o -MF CMakeFiles/ost_gui.dir/gosty_app.cc.o.d -o CMakeFiles/ost_gui.dir/gosty_app.cc.o -c /<>/modules/gui/src/gosty_app.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /<>/modules/gui/src/main_area.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /<>/modules/gui/src/widget_state_saver.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o -MF CMakeFiles/ost_gui.dir/scene_selection.cc.o.d -o CMakeFiles/ost_gui.dir/scene_selection.cc.o -c /<>/modules/gui/src/scene_selection.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /<>/modules/gui/src/gosty_app.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/modules/gui/src/gosty_app.hh:28, from /<>/modules/gui/src/gosty_app.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /<>/modules/gui/src/gosty_app.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -MF CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o.d -o CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -c /<>/modules/gui/src/widget_geom_handler.cc [ 86%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -MF CMakeFiles/_ost_io.dir/export_omf_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_omf_io.cc.o -c /<>/modules/io/pymod/export_omf_io.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -MF CMakeFiles/ost_gui.dir/file_loader.cc.o.d -o CMakeFiles/ost_gui.dir/file_loader.cc.o -c /<>/modules/gui/src/file_loader.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -c /<>/modules/gui/src/panels/button_bar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /<>/modules/gui/src/scene_selection.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_selection.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gui/src/scene_selection.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/drop_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -c /<>/modules/gui/src/panels/drop_box.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, from /<>/modules/io/pymod/export_omf_io.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/io/pymod/export_omf_io.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gui/src/panels/drop_box.hh:22, from /<>/modules/gui/src/panels/drop_box.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/ptr_container/ptr_vector.hpp:19, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -c /<>/modules/gui/src/panels/panel_bar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gui/src/file_loader.hh:24, from /<>/modules/gui/src/file_loader.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/file_loader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/modules/gui/src/file_loader.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -c /<>/modules/gui/src/panels/bottom_bar.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_box.cc.o -c /<>/modules/gui/src/panels/button_box.cc [ 87%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -MF CMakeFiles/_ost_io.dir/export_map_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_map_io.cc.o -c /<>/modules/io/pymod/export_map_io.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gui/src/panels/drop_box.hh:22, from /<>/modules/gui/src/panels/panel_bar.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/panels/panel_bar.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -MF CMakeFiles/ost_gui.dir/panels/event_button.cc.o.d -o CMakeFiles/ost_gui.dir/panels/event_button.cc.o -c /<>/modules/gui/src/panels/event_button.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -c /<>/modules/gui/src/panels/panel_manager.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -c /<>/modules/gui/src/panels/panel_widget_container.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, from /<>/modules/io/pymod/export_map_io.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/io/pymod/export_map_io.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC 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modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -c /<>/modules/gui/src/tools/tool_option.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 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CMakeFiles/ost_gui.dir/tools/tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool.cc.o -c /<>/modules/gui/src/tools/tool.cc [ 88%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/io/_ost_io.so cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/io/_ost_io.so CMakeFiles/_ost_io.dir/wrap_io.cc.o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o CMakeFiles/_ost_io.dir/export_omf_io.cc.o CMakeFiles/_ost_io.dir/export_map_io.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/io/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/io/pymod/remote.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./remote.pyc\",\"remote.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/io/pymod/repository.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/io/./repository.pyc\",\"repository.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 88%] Built target _ost_io make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 88%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -c /<>/modules/mol/mm/pymod/export_forcefield.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -MF CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o.d -o CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -c /<>/modules/gui/src/tools/mouse_event.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -MF CMakeFiles/ost_gui.dir/tools/manipulator.cc.o.d -o CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -c /<>/modules/gui/src/tools/manipulator.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -c /<>/modules/gui/src/tools/tool_options_widget.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -c /<>/modules/gui/src/tools/tool_bar.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /<>/modules/mol/mm/pymod/export_forcefield.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_forcefield.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -c /<>/modules/gui/src/tools/selection_tool.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/tools/manipulator.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/tools/manipulator.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -c /<>/modules/gui/src/tools/measure_tool.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/tools/selection_tool.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25, from /<>/modules/gui/src/tools/selection_tool.hh:26, from /<>/modules/gui/src/tools/selection_tool.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -c /<>/modules/gui/src/python_shell/gutter.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/tools/tool_bar.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/tools/tool_bar.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/modules/gui/src/tools/measure_tool.hh:28, from /<>/modules/gui/src/tools/measure_tool.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:25, from /<>/modules/gui/src/tools/measure_tool.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -c /<>/modules/gui/src/python_shell/main_thread_runner.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -c /<>/modules/gui/src/python_shell/output_redirector.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -c /<>/modules/gui/src/python_shell/dir_model.cc cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -c /<>/modules/gui/src/python_shell/completer_base.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -c /<>/modules/gui/src/python_shell/path_completer.cc /<>/modules/gui/src/python_shell/dir_model.cc: In constructor ‘ost::gui::OstDirModel::OstDirModel(QObject*)’: /<>/modules/gui/src/python_shell/dir_model.cc:31:18: warning: ‘QDirModel::QDirModel(QObject*)’ is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 31 | QDirModel(parent) | ^ In file included from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /<>/modules/gui/src/python_shell/dir_model.hh:26, from /<>/modules/gui/src/python_shell/dir_model.cc:23: /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -c /<>/modules/gui/src/python_shell/python_context_parser.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -c /<>/modules/gui/src/python_shell/python_completer.cc [ 91%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -c /<>/modules/mol/mm/pymod/export_settings.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -c /<>/modules/gui/src/python_shell/python_interpreter.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -c /<>/modules/gui/src/python_shell/python_interpreter_worker.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -c /<>/modules/gui/src/python_shell/python_namespace_tree_model.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /<>/modules/mol/mm/pymod/export_settings.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_settings.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -c /<>/modules/gui/src/python_shell/python_namespace_tree_item.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK 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-fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -c /<>/modules/gui/src/python_shell/python_shell.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -c /<>/modules/gui/src/python_shell/python_shell_widget.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -c /<>/modules/gui/src/python_shell/python_shell_text_document_layout.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -c /<>/modules/gui/src/python_shell/python_tokenizer.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -c /<>/modules/gui/src/python_shell/python_syntax_highlighter.cc [ 91%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS 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Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -c /<>/modules/gui/src/python_shell/shell_history.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK 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-DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -MF 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/usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -c /<>/modules/gui/src/python_shell/state_machine.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state.cc.o -c /<>/modules/gui/src/python_shell/state.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -c /<>/modules/gui/src/python_shell/transition.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /<>/modules/mol/mm/pymod/export_simulation.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_simulation.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -c /<>/modules/gui/src/python_shell/transition_guard.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -c /<>/modules/gui/src/scene_win/context_menu.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -c /<>/modules/gui/src/scene_win/current_selection_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/scene_win/context_menu.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/pointer_cast.hpp:52, from /<>/modules/gui/src/scene_win/context_menu.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -c /<>/modules/gui/src/scene_win/custom_part_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_iso.hh:33, from /<>/modules/gui/src/scene_win/context_menu.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ In file included from /<>/modules/gui/src/scene_win/entity_node.hh:28, from /<>/modules/gui/src/scene_win/context_menu.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 92%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -c /<>/modules/mol/mm/pymod/export_openmm.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -c /<>/modules/gui/src/scene_win/scene_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/scene_win/custom_part_node.hh:23, from /<>/modules/gui/src/scene_win/custom_part_node.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/scene_win/custom_part_node.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/scene_win/current_selection_node.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_win/current_selection_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -c /<>/modules/gui/src/scene_win/label_node.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -c /<>/modules/gui/src/scene_win/entity_node.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -c /<>/modules/gui/src/scene_win/entity_part_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /<>/modules/gui/src/scene_win/label_node.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/scene_win/label_node.hh:23, from /<>/modules/gui/src/scene_win/label_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/scene_win/entity_part_node.hh:23, from /<>/modules/gui/src/scene_win/entity_part_node.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -c /<>/modules/gui/src/scene_win/gfx_scene_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/scene_win/entity_part_node.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ [ 93%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -c /<>/modules/mol/mm/pymod/export_observers.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/gui/src/scene_win/entity_node.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_win/entity_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -c /<>/modules/gui/src/scene_win/render_mode_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /<>/modules/gui/src/scene_win/gfx_scene_node.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node_fw.hh:25, from /<>/modules/gui/src/scene_win/gfx_scene_node.hh:23, from /<>/modules/gui/src/scene_win/gfx_scene_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -c /<>/modules/gui/src/scene_win/render_modes_node.cc [ 93%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -c /<>/modules/mol/mm/pymod/export_ff_reader.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/scene_win/render_mode_node.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/scene_win/render_mode_node.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /<>/modules/mol/mm/pymod/export_observers.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_observers.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -c /<>/modules/gui/src/scene_win/root_node.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/scene_win/render_modes_node.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_win/render_modes_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /<>/modules/gui/src/scene_win/root_node.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/scene_win/root_node.hh:23, from /<>/modules/gui/src/scene_win/root_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /<>/modules/mol/mm/pymod/export_ff_reader.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_ff_reader.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -c /<>/modules/mol/mm/pymod/export_interaction.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:41, from /<>/modules/gui/src/scene_win/render_modes_node.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: ‘virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)’ was hidden [-Woverloaded-virtual=] 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); | ^~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by ‘ost::gfx::Entity::Apply’ 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); | ^~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -c /<>/modules/gui/src/scene_win/scene_win.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -c /<>/modules/gui/src/scene_win/scene_win_model.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/modules/gui/src/scene_win/scene_win_model.hh:28, from /<>/modules/gui/src/scene_win/scene_win_model.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /<>/modules/gui/src/scene_win/scene_win_model.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -c /<>/modules/mol/mm/pymod/export_buildingblock.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/modules/mol/mm/pymod/export_interaction.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_interaction.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gui/src/scene_win/scene_win_model.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: ‘virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void DeepSwap(GfxNode& n); | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by ‘virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)’ 58 | virtual void DeepSwap(GfxObj& go); | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /<>/modules/gui/src/scene_win/scene_win.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/scene_win/scene_win.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/modules/gui/src/scene_win/scene_win.cc: In member function ‘void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)’: /<>/modules/gui/src/scene_win/scene_win.cc:117:31: warning: ‘QModelIndex QModelIndex::child(int, int) const’ is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations] 117 | model->select(parent.child(start,0),QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Rows); | ~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/qt5/QtCore/QModelIndex:1, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, from /<>/modules/gui/src/scene_win/scene_win.cc:26: /usr/include/aarch64-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const | ^~~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/map_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -c /<>/modules/gui/src/tools/map_tool.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -c /<>/modules/gui/src/data_viewer/argand.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /<>/modules/mol/mm/pymod/export_buildingblock.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_buildingblock.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/modules/gui/src/data_viewer/argand.hh:30, from /<>/modules/gui/src/data_viewer/argand.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/gui/src/data_viewer/argand.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -c /<>/modules/mol/mm/pymod/export_block_modifiers.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -c /<>/modules/gui/src/data_viewer/data_viewer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, from /<>/modules/gui/src/tools/map_tool.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/platform.hh:22, from /<>/modules/gui/src/tools/map_tool.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -c /<>/modules/mol/mm/pymod/export_topology.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /<>/modules/mol/mm/pymod/export_block_modifiers.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_block_modifiers.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -c /<>/modules/gui/src/data_viewer/data_viewer_panel.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /<>/modules/gui/src/data_viewer/data_viewer.cc:36: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /<>/modules/gui/src/data_viewer/data_viewer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /<>/modules/gui/src/data_viewer/data_viewer_panel.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /<>/modules/mol/mm/pymod/export_topology.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_topology.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -c /<>/modules/gui/src/data_viewer/data_viewer_panel_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /<>/modules/mol/mm/pymod/export_topology.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -c /<>/modules/gui/src/data_viewer/draw_overlay.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /<>/modules/gui/src/data_viewer/draw_overlay.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o -c /<>/modules/mol/mm/pymod/export_modeller.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -c /<>/modules/gui/src/data_viewer/drawing_functions.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -c /<>/modules/gui/src/data_viewer/fft_panel.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gui/src/data_viewer/drawing_functions.hh:28, from /<>/modules/gui/src/data_viewer/drawing_functions.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /<>/modules/gui/src/data_viewer/drawing_functions.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /<>/modules/gui/src/data_viewer/fft_panel.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /<>/modules/mol/mm/pymod/export_modeller.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/mol/mm/pymod/export_modeller.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/modules/mol/mm/pymod/export_modeller.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -c /<>/modules/gui/src/data_viewer/info_panel.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -c /<>/modules/gui/src/data_viewer/img2qt.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/gui/src/data_viewer/info_panel.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /usr/include/boost/format.hpp:17, from /<>/modules/gui/src/data_viewer/info_panel.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -c /<>/modules/mol/mm/pymod/wrap_mol_mm.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/modules/gui/src/data_viewer/img2qt.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -c /<>/modules/gui/src/data_viewer/mask_overlay.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -c /<>/modules/gui/src/data_viewer/null_overlay.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -c /<>/modules/gui/src/data_viewer/overlay_base.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, from /<>/modules/gui/src/data_viewer/mask_overlay.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -c /<>/modules/gui/src/data_viewer/overlay_manager.cc [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -c /<>/modules/gui/src/data_viewer/overlay_manager_gui.cc [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -c /<>/modules/gui/src/data_viewer/pointlist_overlay.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /<>/modules/gui/src/data_viewer/overlay_manager.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/gui/src/data_viewer/overlay_manager.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /<>/modules/gui/src/data_viewer/pointlist_overlay.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /<>/modules/gui/src/data_viewer/pointlist_overlay.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -c /<>/modules/gui/src/data_viewer/pointlist_overlay_base.cc [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -c /<>/modules/gui/src/data_viewer/strategies.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /<>/modules/gui/src/data_viewer/pointlist_overlay_base.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /<>/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/gui/src/data_viewer/strategies.hh:29, from /<>/modules/gui/src/data_viewer/strategies.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -c /<>/modules/gui/src/data_viewer/viewer_normalizer.cc /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Linking CXX shared module ../../../../stage/lib/python3.12/dist-packages/ost/mol/mm/_ost_mol_mm.so cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../../stage/lib/python3.12/dist-packages/ost/mol/mm/_ost_mol_mm.so CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_mm.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../stage/lib/libost_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libOpenMM.so cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/mm/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/mol/mm/pymod/antechamber.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/mol/mm/./antechamber.pyc\",\"antechamber.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target _ost_mol_mm In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /<>/modules/gui/src/data_viewer/viewer_normalizer.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/gui/src/data_viewer/viewer_normalizer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Linking CXX shared library ../../../stage/lib/libost_gui.so cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. 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/usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gui.so.2.5.0 ../../../stage/lib/libost_gui.so.2.5 ../../../stage/lib/libost_gui.so make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target ost_gui make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/depend make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/pymod /<>/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake "--color=" [ 97%] Generating moc_gosty.cpp [ 97%] Generating qrc_dngr.cpp cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty.cpp_parameters make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/rcc --name dngr --output /<>/obj-aarch64-linux-gnu/modules/gui/src/qrc_dngr.cpp /<>/modules/gui/src/dngr.qrc make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -MF CMakeFiles/_ost_gui.dir/wrap_gui.cc.o.d -o CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -c /<>/modules/gui/pymod/wrap_gui.cc cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -MF CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o.d -o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -c /<>/modules/gui/pymod/export_alignment_view.cc cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/src /<>/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/gosty.dir/DependInfo.cmake "--color=" [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_message_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -c /<>/modules/gui/pymod/export_message_widget.cc make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 97%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o -MF CMakeFiles/gosty.dir/gosty.cc.o.d -o CMakeFiles/gosty.dir/gosty.cc.o -c /<>/modules/gui/src/gosty.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /<>/modules/gui/pymod/export_alignment_view.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_alignment_view.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -c /<>/modules/gui/pymod/export_gl_win.cc [ 97%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o -MF CMakeFiles/gosty.dir/moc_gosty.cpp.o.d -o CMakeFiles/gosty.dir/moc_gosty.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty.cpp [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -MF CMakeFiles/_ost_gui.dir/export_tool.cc.o.d -o CMakeFiles/_ost_gui.dir/export_tool.cc.o -c /<>/modules/gui/pymod/export_tool.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -MF CMakeFiles/_ost_gui.dir/export_py_shell.cc.o.d -o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -c /<>/modules/gui/pymod/export_py_shell.cc [ 97%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o -MF CMakeFiles/gosty.dir/qrc_dngr.cpp.o.d -o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -c /<>/obj-aarch64-linux-gnu/modules/gui/src/qrc_dngr.cpp [ 97%] Linking CXX executable ../../../stage/lib/openstructure/libexec/gosty cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gosty.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/gosty.dir/gosty.cc.o CMakeFiles/gosty.dir/moc_gosty.cpp.o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -o ../../../stage/lib/openstructure/libexec/gosty -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_gfx.so.2.5.0 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.5.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target gosty [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -MF CMakeFiles/_ost_gui.dir/export_gosty.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gosty.cc.o -c /<>/modules/gui/pymod/export_gosty.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -c /<>/modules/gui/pymod/export_scene_win.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -c /<>/modules/gui/pymod/export_sequence_viewer.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /<>/modules/gui/pymod/export_gosty.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_gosty.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /<>/modules/gui/pymod/export_gosty.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /<>/modules/gui/pymod/export_scene_win.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_scene_win.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /<>/modules/gui/pymod/export_sequence_viewer.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_sequence_viewer.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -MF CMakeFiles/_ost_gui.dir/export_perspective.cc.o.d -o CMakeFiles/_ost_gui.dir/export_perspective.cc.o -c /<>/modules/gui/pymod/export_perspective.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -MF CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -c /<>/modules/gui/pymod/export_sip_handler.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -c /<>/modules/gui/pymod/export_scene_selection.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -MF CMakeFiles/_ost_gui.dir/export_main_area.cc.o.d -o CMakeFiles/_ost_gui.dir/export_main_area.cc.o -c /<>/modules/gui/pymod/export_main_area.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -MF CMakeFiles/_ost_gui.dir/export_panels.cc.o.d -o CMakeFiles/_ost_gui.dir/export_panels.cc.o -c /<>/modules/gui/pymod/export_panels.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /<>/modules/gui/pymod/export_scene_selection.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_scene_selection.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -MF CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o.d -o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -c /<>/modules/gui/pymod/export_menu_bar.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_loader.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -c /<>/modules/gui/pymod/export_file_loader.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -c /<>/modules/gui/pymod/export_file_viewer.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_widget.cc.o -c /<>/modules/gui/pymod/export_widget.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /<>/modules/gui/pymod/export_file_loader.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_file_loader.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -c /<>/modules/gui/pymod/export_gl_canvas.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -MF CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o.d -o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -c /<>/modules/gui/pymod/data_viewer_proxy.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -c /<>/modules/gui/pymod/export_data_viewer.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay.cc.o -c /<>/modules/gui/pymod/export_overlay.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.12 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -c /<>/modules/gui/pymod/export_overlay_manager.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/modules/gui/pymod/data_viewer_proxy.hh:35, from /<>/modules/gui/pymod/data_viewer_proxy.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/sip_handler.hh:22, from /<>/modules/gui/pymod/data_viewer_proxy.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, from /<>/modules/gui/pymod/export_data_viewer.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_data_viewer.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh:28, from /<>/modules/gui/pymod/export_overlay.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, from /usr/include/python3.12/pyport.h:195, from /usr/include/python3.12/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, from /<>/modules/gui/pymod/export_overlay.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX shared module ../../../stage/lib/python3.12/dist-packages/ost/gui/_ost_gui.so cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/presets.xml /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/presets.xml cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/icons/color_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/color_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/icons/preset_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/preset_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/icons/render_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/render_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /<>/modules/gui/pymod/scene/icons/tool_icon.png /<>/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/tool_icon.png cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o ../../../stage/lib/python3.12/dist-packages/ost/gui/_ost_gui.so CMakeFiles/_ost_gui.dir/wrap_gui.cc.o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o CMakeFiles/_ost_gui.dir/export_tool.cc.o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o CMakeFiles/_ost_gui.dir/export_gosty.cc.o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o CMakeFiles/_ost_gui.dir/export_perspective.cc.o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o CMakeFiles/_ost_gui.dir/export_main_area.cc.o CMakeFiles/_ost_gui.dir/export_panels.cc.o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o CMakeFiles/_ost_gui.dir/export_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o CMakeFiles/_ost_gui.dir/export_overlay.cc.o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.5.0 /usr/lib/aarch64-linux-gnu/libpython3.12.so /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../stage/lib/libost_gfx.so.2.5.0 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.5.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/color_options_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_options_widget.pyc\",\"color_options_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/color_select_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/color_select_widget.pyc\",\"color_select_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/combo_options_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/combo_options_widget.pyc\",\"combo_options_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/cpk_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/cpk_widget.pyc\",\"cpk_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/custom_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/custom_widget.pyc\",\"custom_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/gradient_editor_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_editor_widget.pyc\",\"gradient_editor_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/gradient_info_handler.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_info_handler.pyc\",\"gradient_info_handler.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/gradient_list_model.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_list_model.pyc\",\"gradient_list_model.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/gradient_preset_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/gradient_preset_widget.pyc\",\"gradient_preset_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/hsc_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/hsc_widget.pyc\",\"hsc_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/immutable_gradient_info_handler.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_gradient_info_handler.pyc\",\"immutable_gradient_info_handler.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/immutable_preset_info_handler.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/immutable_preset_info_handler.pyc\",\"immutable_preset_info_handler.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/init_inspector.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/init_inspector.pyc\",\"init_inspector.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/inspector_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/inspector_widget.pyc\",\"inspector_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/map_level_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/map_level_widget.pyc\",\"map_level_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset.pyc\",\"preset.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/remote.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/remote.pyc\",\"remote.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset_editor_list_model.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_list_model.pyc\",\"preset_editor_list_model.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset_editor_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_editor_widget.pyc\",\"preset_editor_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset_info_handler.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_info_handler.pyc\",\"preset_info_handler.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset_list_model.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_list_model.pyc\",\"preset_list_model.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/preset_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/preset_widget.pyc\",\"preset_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/render_mode_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_mode_widget.pyc\",\"render_mode_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/render_op.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_op.pyc\",\"render_op.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/render_options_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/render_options_widget.pyc\",\"render_options_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/scene_observer_impl.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_observer_impl.pyc\",\"scene_observer_impl.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/scene_selection_helper.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/scene_selection_helper.pyc\",\"scene_selection_helper.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/simple_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/simple_widget.pyc\",\"simple_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/sline_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/sline_widget.pyc\",\"sline_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/toolbar_options_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/toolbar_options_widget.pyc\",\"toolbar_options_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/trace_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/trace_widget.pyc\",\"trace_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/tube_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/tube_widget.pyc\",\"tube_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/uniform_color_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/uniform_color_widget.pyc\",\"uniform_color_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/visibility_op.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/visibility_op.pyc\",\"visibility_op.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/line_trace_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/line_trace_widget.pyc\",\"line_trace_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/wireframe_widget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/wireframe_widget.pyc\",\"wireframe_widget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/scene/query_editor.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/scene/query_editor.pyc\",\"query_editor.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/dng/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/dng/termuse.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/termuse.pyc\",\"termuse.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/dng/superpositiondialog.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/superpositiondialog.pyc\",\"superpositiondialog.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/dng/init.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/init.pyc\",\"init.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/dng/menu.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/dng/menu.pyc\",\"menu.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/__init__.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/init_context_menu.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_context_menu.pyc\",\"init_context_menu.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/init_menubar.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_menubar.pyc\",\"init_menubar.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/init_spacenav.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_spacenav.pyc\",\"init_spacenav.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/init_splash.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./init_splash.pyc\",\"init_splash.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/trajectory_viewer.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./trajectory_viewer.pyc\",\"trajectory_viewer.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/helpwidget.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./helpwidget.pyc\",\"helpwidget.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/table.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./table.pyc\",\"table.py\",doraise=True)" cd /<>/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/<>/modules/gui/pymod/gosty_startup.py\",\"/<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/gui/./gosty_startup.pyc\",\"gosty_startup.py\",doraise=True)" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target _ost_gui make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /<>/obj-aarch64-linux-gnu/stage/bin/ost cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /<>/obj-aarch64-linux-gnu/stage/bin/dng cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/ost_startup.py cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /<>/scripts/dng_startup.py /<>/obj-aarch64-linux-gnu/stage/lib/python3.12/dist-packages//ost/dng_startup.py make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target ost_scripts make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-aarch64-linux-gnu' dh_auto_test -a cd obj-aarch64-linux-gnu && make -j4 check ARGS\+=--verbose ARGS\+=-j4 make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 93 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/lib make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/bin [ 0%] Built target subst_ost_startup.py [ 0%] Built target subst_ost make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/scripts /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/scripts /<>/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/<>/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.12.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.12/dist-packages/ -P /<>/cmake_support/substitute.cmake [ 0%] Built target subst_ost_config cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /<>/obj-aarch64-linux-gnu/tests make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target subst_dng [ 0%] Built target create_stage make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/src /<>/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake "--color=" make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/src /<>/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/config /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/config /<>/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./alignment_opts.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./base.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/export_helper/vector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/generic_property_def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./config.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./def.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./clip_alignment.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./dllexport.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./dllexport.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/pair_to_tuple_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./exc.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./exc.hh cd /<>/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /<>/modules/config/./version.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./version.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./conservation.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/export_helper/vec_to_list_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./contact_prediction_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./geom.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./geom.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/test_utils/compare_files.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat.hh [ 0%] Built target ost_config_headers cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./contact_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/src /<>/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat2.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./distance_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./generic_property.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./generic_property.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat3.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./integrity_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./integrity_error.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./entropy.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_error.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./mat4.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./invalid_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./global_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./ins_del.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./ptr_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec2.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./local_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./log.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./log.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./merge_pairwise_alignments.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./log_sink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./log_sink.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec4.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_group.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat2_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_item.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_item.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./profile.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./pair_subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat3_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./dyn_cast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./semiglobal_align.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./stdint.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./stdint.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vecmat4_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./sequence_identity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./circular_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./stdint_msc.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./constants.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./constants.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./sequence_similarity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_path.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_path.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./range.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./range.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_set.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_set.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite2.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./units.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./units.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./variance_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite3.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./message.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./message.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./info_verbose_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./platform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./platform.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./item_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite2_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./string_ref.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./string_ref.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./hmm_pseudo_counts.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./geom_info_conversion.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./composite3_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/alg/src/./hmm_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./pod_vector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./pod_vector.hh cd /<>/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /<>/modules/info/src/./item_type_cast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type_cast.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./aligned_cuboid.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./fixed_string.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./fixed_string.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_seq_alg_headers make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./tri_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./tri_matrix.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/src /<>/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./vec_mat_predicates.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh [ 0%] Built target ost_info_headers make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/src /<>/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./boost_filesystem_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./quat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./quat.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/pointer_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/base/src/./paged_array.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/./paged_array.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./point_cloud.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./point_cloud.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /<>/modules/geom/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/./module_config.hh [ 0%] Built target ost_base_headers make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/src /<>/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake "--color=" [ 0%] Built target ost_geom_headers cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/atom_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/impl/sequence_list_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/src /<>/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./conop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./conop.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/chain_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_list.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./sqlite_wrap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/chain_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./processor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./processor.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./sqlite_conv.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./alignment_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/connector_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./amino_acids.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./diag.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./diag.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/connector_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./linear_indexer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./model_check.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./sequence_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/dihedral.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./binary_container.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_region.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./heuristic.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/entity_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /<>/modules/db/src/./extract_data_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_column.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/entity_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/fragment_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./aligned_column_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound_lib.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib.hh [ 0%] Built target ost_db_headers make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/fragment_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./invalid_sequence.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/src /<>/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_ast.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./views_from_sequences.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./rule_based.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_ast_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/seq/base/src/./profile_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen_s.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./minimal_compound_lib.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./compound_lib_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_gen_s.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 0%] Built target ost_seq_headers cd /<>/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /<>/modules/conop/src/./ring_finder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/./ring_finder.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_iso_spec.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/src /<>/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/query_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/map_octree.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/residue_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/octree_isocont.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh [ 0%] Built target ost_conop_headers make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/residue_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/src /<>/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/raster_image/raster_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/cartoon_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/dispatch.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/surface_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/custom_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./anisotropic.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/surface_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./auto_correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/cpk_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/torsion_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/debug_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./clear.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/impl/torsion_impl_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/simple_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/sline_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./clip_min_max.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/trace_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./conjugate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_def.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./convolute.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/line_trace_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./atom_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_frequency_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/backbone_trace.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./cross_correlate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bond_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./density_slice.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_detail.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bond_table.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./dft.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_renderer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_spatial_domain.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/trace_renderer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fft.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/connect_renderer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fftw_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fill.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/mapped_property.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/image_state_visitor_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chain_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./filter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/entity_renderer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chem_class.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/index.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/tabulated_trig.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fourier_filters.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./chem_type.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/impl/fast_spheres.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/image_state/value_holder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian_gradient_magnitude.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/line_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./circle_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./in_mem_coord_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./gaussian_laplacian.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/custom_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./coord_frame.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./composite_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/cpk_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./highest_peak_search_3d.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./editor_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_algorithm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/simple_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./editor_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./histogram.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/sline_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./mol.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./mol.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data_types.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data_types.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./line_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/line_trace_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./data.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./data.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./local_sigma_threshold.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/cartoon_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./mask_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./debug.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./debug.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./dllexport.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./dllexport.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./negate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/render_options/trace_render_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent_iterator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./normalizer_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_observer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/by_element_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./normalizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./extent.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./extent.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/by_chain_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_property_mapper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_linear.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_factory.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_log.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/uniform_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./norm_od.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/gradient_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_handle_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./entity_visitor_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./power_spectrum.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./handle_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/entity_view_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./randomize.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./ics_editor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./smooth_mask_image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/basic_gradient_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./not_connected_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_list.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/gradient_level_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_state_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./property_id.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/color_ops/map_handle_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat_accumulator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./render_pass.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./image.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./image.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./stat_min_max.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./bitmap_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_error.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./inverted_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./threshold.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./collada_exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./map.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transcendentals.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./color.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./color.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transform_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./entity_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gl_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_mirror.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./residue_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./alg_shift.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./sec_structure.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./discrete_shrink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./spatial_organizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transformation_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./normalizer_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./transformations.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_node_visitor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./normalizer_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_builder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./fractional_shift.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./null_data.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./null_data.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./builder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./builder.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./observable.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./observable.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_object_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./polar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./surface_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./paste_impl.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_prim.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./line_average.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./peak.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./peak.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./torsion_handle.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /<>/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/alg/src/./rscrosscorr.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./symmetry_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./transfer_connectivity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./phase.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./phase.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gfx_test_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./query_view_wrapper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./physical_units.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./glwin_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh [ 0%] Built target ost_img_alg_headers cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./pixel_sampling.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/src /<>/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./input.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./input.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_type_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./point_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./point_list.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./prim_list.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_option_group.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./view_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./point.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./point.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./scene.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./xcs_editor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./polygon_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./selection.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./bounding_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./progress.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./progress.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/selection_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./transform.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./transform.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./size.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./size.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./texture.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/base/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./spherical_mask.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/measure_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./vertex_array.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./util.cc /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./util.cc [ 0%] Built target ost_mol_headers cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./vertex_array_helper.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/src /<>/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_option.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./util.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./scene_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./value_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./value_util.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gl_include.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/chemdict_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./vecmat.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./glext_include.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/star_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /<>/modules/img/base/src/./mask_info_convert.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./render_mode.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/manipulator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./material.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./material.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/tool_options_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh [ 0%] Built target ost_img_headers make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gradient.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/mouse_event.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/src /<>/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/io_profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/tools/map_tool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gradient_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./svd_superpose.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/align_properties_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/dcd_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/base_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./primitives.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_crd_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/background_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./sec_structure_segments.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./povray_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_pqr_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/conservation_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./local_dist_diff_test.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./povray.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_mae_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./distance_test_common.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/secstr_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_mmcif_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./distance_rmsd_test.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./exporter_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./superpose_frames.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_selection_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./gost_exporter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./filter_clashes.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/seq_text_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./construct_cbeta.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./color_ops/map_handle_color_op.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_pdb_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_delegate.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./clash_score.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_iso.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_slab.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./trajectory_analysis.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/entity_io_sdf_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./structure_analysis.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_search_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /<>/modules/gfx/src/./map_iso_prop.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./consistency_checks.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_table_view.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./pdbize.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/save_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh [ 0%] Built target ost_gfx_headers make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/src /<>/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./adjacency_bitmap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/load_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/tick_painter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/title_row.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./consistency_checks.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/surface_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /<>/modules/bindings/src/./wrap_tmalign.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/alignment_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/load_surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_surface.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./contact_overlap.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/base_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/surface_io_msms_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh [ 0%] Built target ost_bindings_headers make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/src /<>/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./domain_find.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/sequence_viewer/sequence_view_object.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/pdb_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./forcefield.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/main_thread_runner.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./similarity_matrix.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/sdf_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./ff_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/output_redirector.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./accessibility.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/mmcif_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./buildingblock.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/completer_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/stereochemical_params_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./sec_struct.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/mol/omf.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./gromacs_block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/dir_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./nonstandard.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./heuristic_block_modifiers.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/load_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/gutter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./molck.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./interaction.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/path_completer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_df3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./find_membrane.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./settings.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./settings.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_context_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/alg/src/./entity_to_density.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/image_format.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./simulation.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_completer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dx_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./modeller.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_spi_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh [ 0%] Built target ost_mol_alg_headers make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/config /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/config /<>/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_situs_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./state_extractor.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_mrc_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh [ 0%] Built target ost_config make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./system_creator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_tokenizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/src /<>/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./topology_creator.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dat_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_syntax_highlighter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./index.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_ipl_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/text_logger.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./topology.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_jpk_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_interpreter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /<>/modules/mol/mm/src/./steep.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_nanoscope_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_interpreter_worker.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_png_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/python_shell_text_document_layout.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build [ 0%] Built target ost_mol_mm_headers make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/src/CMakeFiles/ost_geom.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_dm3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/shell_history.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh [ 1%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/src /<>/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/pymod /<>/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/map_io_tiff_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/state_machine.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/tiff_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/state.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/img/jpk_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/jpk_util.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/transition.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/sequence_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/python_shell/transition_guard.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/fasta_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh [ 2%] Built target ost_base make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/depend cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/button_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/tests /<>/obj-aarch64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/pir_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/drop_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/promod_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/profile_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -c /<>/modules/geom/tests/test_composite3.cc cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/hhm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/pssm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/bottom_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/clustal_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/button_box.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_box.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/event_button.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/load.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/pymod/CMakeFiles/_ost_geom.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_widget_container.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/seq/save.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/save.hh [ 4%] Built target _ost_geom make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./binary_data_sink.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/src /<>/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/panel_bar_widget_holder.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/side_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/splitter_panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./binary_data_source.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./module_config.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./container_serialization.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/panels/tabbed_panel_bar.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/info/src/CMakeFiles/ost_info.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./swap_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/context_menu.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh [ 5%] Built target ost_info make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/pymod /<>/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_utils.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/current_selection_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./io_exception.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/custom_part_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./convert.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./convert.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/entity_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./converting_streams.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./converting_streams.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/entity_part_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./formatted_line.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/gfx_scene_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/chemdict_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/label_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/star_parser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/root_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/render_mode_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/base/pymod/CMakeFiles/_ost_base.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_info.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/render_modes_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh [ 5%] Built target _ost_base make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/src /<>/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_node.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/io_profile.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/dcd_io.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/scene_win/scene_win_model.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_crd_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/message_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_pqr_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/message_box_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_mae_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/messages/log_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_mmcif_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/argand.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_reader.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/src/CMakeFiles/ost_img.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_pdb_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh [ 8%] Built target ost_img make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/src /<>/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/data_viewer_panel_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/entity_io_sdf_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/draw_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/drawing_functions.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_writer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/fft_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/save_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/info_panel.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/load_entity.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/img2qt.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/surface_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/mask_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/load_surface.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/null_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/surface_io_msms_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/pdb_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/sdf_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_str.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/mmcif_str.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_str.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_base_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/stereochemical_params_reader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./mol/omf.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./omf.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_gui.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/sequence_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/overlay_manager_observer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/fasta_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/pointlist_overlay.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/pir_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/pointlist_overlay_base.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/promod_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/strategies.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/profile_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/strategies_fw.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/hhm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/pssm_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/data_viewer/viewer_normalizer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/clustal_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_browser.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_browser.hh [ 13%] Built target ost_mol make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/info/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/info/pymod /<>/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/load.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_type_dialog.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./seq/save.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./save.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_viewer.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/load_map.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./load_map.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gl_canvas.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_df3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/image_format.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./image_format.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gl_win.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_win.hh make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dx_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh [ 13%] Built target _ost_info cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./scene_menu.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_menu.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/src /<>/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_spi_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./gosty_app.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_situs_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./admin.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./admin.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./module_config.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_mrc_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dat_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main_area.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_ipl_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./perspective.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_jpk_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./scene_selection.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./main_window.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_nanoscope_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_png_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./dock_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_dm3_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./dock_widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/map_io_tiff_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./thin_splitter.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/tiff_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./tiff_util.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget.hh cd /<>/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /<>/modules/io/src/./img/jpk_util.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_geom_handler.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 13%] Built target ost_io_headers make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/pymod /<>/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_pool.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_pool.hh [ 18%] Built target ost_img_alg cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_registry.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_registry.hh make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/tests /<>/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake "--color=" cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./widget_state_saver.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /<>/modules/gui/src/./file_loader.hh /<>/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_loader.hh [ 18%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -MF CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -c /<>/modules/base/tests/test_generic_property.cc make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 18%] Built target ost_gui_headers make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/tests /<>/obj-aarch64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 18%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o -MF CMakeFiles/ost_img_tests.dir/test_data.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_data.cc.o -c /<>/modules/img/base/tests/test_data.cc make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 19%] Built target _ost_img make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/tests /<>/obj-aarch64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 19%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -c /<>/modules/img/alg/tests/test_clear.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_composite3.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/modules/geom/tests/test_composite3.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/modules/img/base/tests/test_data.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/img/base/tests/test_data.hh:29, from /<>/modules/img/base/tests/test_data.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_clear.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_clear.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/base/tests/test_generic_property.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/base/tests/test_generic_property.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 19%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o -MF CMakeFiles/ost_img_tests.dir/test_extent.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_extent.cc.o -c /<>/modules/img/base/tests/test_extent.cc [ 19%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -c /<>/modules/img/alg/tests/test_conj.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/base/tests/test_extent.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/base/tests/test_extent.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_conj.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_conj.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -c /<>/modules/geom/tests/test_composite2.cc [ 20%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image.cc.o -c /<>/modules/img/base/tests/test_image.cc [ 20%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -MF CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -c /<>/modules/base/tests/test_string_ref.cc [ 20%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -c /<>/modules/img/alg/tests/test_convolute.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_composite2.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/base/tests/test_image.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/base/tests/test_image.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_convolute.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_convolute.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -c /<>/modules/img/alg/tests/test_discrete_shrink.cc [ 20%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -c /<>/modules/geom/tests/test_mat2.cc [ 20%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -MF CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -c /<>/modules/base/tests/test_pod_vector.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_discrete_shrink.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_discrete_shrink.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_mat2.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -c /<>/modules/img/alg/tests/test_fft.cc [ 20%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -c /<>/modules/img/base/tests/test_image_state.cc [ 20%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -c /<>/modules/geom/tests/test_mat3.cc [ 20%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o -MF CMakeFiles/ost_base_tests.dir/tests.cc.o.d -o CMakeFiles/ost_base_tests.dir/tests.cc.o -c /<>/modules/base/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/alg/tests/test_fft.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/modules/img/alg/tests/test_fft.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_mat3.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /<>/modules/img/base/tests/test_image_state.cc:32: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/img/base/tests/test_image_state.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Linking CXX executable ../../../tests/ost_base_tests cd /<>/obj-aarch64-linux-gnu/modules/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o CMakeFiles/ost_base_tests.dir/tests.cc.o -o ../../../tests/ost_base_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 20%] Built target ost_base_tests make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/tests /<>/obj-aarch64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 20%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -c /<>/modules/mol/base/tests/test_atom_groups.cc [ 20%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -c /<>/modules/geom/tests/test_mat4.cc [ 20%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -c /<>/modules/img/base/tests/test_image_state_visitor.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_atom_groups.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_atom_groups.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_mat4.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -c /<>/modules/img/alg/tests/test_fill.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /<>/modules/img/base/tests/test_image_state_visitor.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/img/base/tests/test_image_state_visitor.hh:29, from /<>/modules/img/base/tests/test_image_state_visitor.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -c /<>/modules/geom/tests/test_op2.cc [ 20%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o -MF CMakeFiles/ost_img_tests.dir/test_index.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_index.cc.o -c /<>/modules/img/base/tests/test_index.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_fill.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_fill.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_chain.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -c /<>/modules/mol/base/tests/test_chain.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_op2.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -c /<>/modules/img/alg/tests/test_filter.cc [ 21%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -MF CMakeFiles/ost_img_tests.dir/test_point.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_point.cc.o -c /<>/modules/img/base/tests/test_point.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_chain.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_chain.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -c /<>/modules/geom/tests/test_op3.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_filter.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/img/alg/tests/test_filter.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/modules/img/base/tests/test_point.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/img/base/tests/test_point.hh:29, from /<>/modules/img/base/tests/test_point.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -MF CMakeFiles/ost_img_tests.dir/test_sampling.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -c /<>/modules/img/base/tests/test_sampling.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_op3.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /<>/modules/img/base/tests/test_sampling.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/img/base/tests/test_sampling.hh:29, from /<>/modules/img/base/tests/test_sampling.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -c /<>/modules/geom/tests/test_op4.cc [ 21%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -MF CMakeFiles/ost_img_tests.dir/test_domains.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_domains.cc.o -c /<>/modules/img/base/tests/test_domains.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_op4.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh:31, from /<>/modules/img/base/tests/test_domains.cc:31: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /<>/modules/img/base/tests/test_domains.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_quat.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -c /<>/modules/geom/tests/test_quat.cc [ 21%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -c /<>/modules/img/alg/tests/test_histogram.cc In file included from /usr/include/c++/13/string:54: In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void mol_base::throw_invalid_chain_handle::test_method()’ at /<>/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function ‘void mol_base::throw_invalid_chain_handle::test_method()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/string:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void mol_base::throw_invalid_chain_handle::test_method()’ at /<>/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void mol_base::throw_invalid_chain_handle::test_method()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void mol_base::throw_invalid_chain_handle::test_method()’ at /<>/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void mol_base::throw_invalid_chain_handle::test_method()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from ‘void mol_base::throw_invalid_chain_handle::test_method()’ at /<>/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function ‘void mol_base::throw_invalid_chain_handle::test_method()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 22%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o -MF CMakeFiles/ost_img_tests.dir/test_size.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_size.cc.o -c /<>/modules/img/base/tests/test_size.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_quat.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_conn.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -c /<>/modules/mol/base/tests/test_conn.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, from /<>/modules/img/alg/tests/test_histogram.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_histogram.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -MF CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -c /<>/modules/img/base/tests/test_value_holder.cc [ 22%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -c /<>/modules/geom/tests/test_vec2.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_conn.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_conn.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -c /<>/modules/img/alg/tests/test_mirror.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_vec2.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -c /<>/modules/mol/base/tests/test_coord_group.cc [ 22%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_tests.dir/tests.cc.o -c /<>/modules/img/base/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_mirror.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_mirror.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -c /<>/modules/geom/tests/test_vec3.cc [ 22%] Linking CXX executable ../../../../tests/ost_img_tests cd /<>/obj-aarch64-linux-gnu/modules/img/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_img_tests.dir/test_data.cc.o CMakeFiles/ost_img_tests.dir/test_extent.cc.o CMakeFiles/ost_img_tests.dir/test_image.cc.o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o CMakeFiles/ost_img_tests.dir/test_index.cc.o CMakeFiles/ost_img_tests.dir/test_point.cc.o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o CMakeFiles/ost_img_tests.dir/test_domains.cc.o CMakeFiles/ost_img_tests.dir/test_size.cc.o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o CMakeFiles/ost_img_tests.dir/tests.cc.o -o ../../../../tests/ost_img_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_coord_group.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_coord_group.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -c /<>/modules/img/alg/tests/test_negate.cc make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 22%] Built target ost_img_tests make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/src /<>/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 23%] Built target ost_seq make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod /<>/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 25%] Built target _ost_mol make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/src /<>/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 26%] Built target ost_db make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod /<>/obj-aarch64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 27%] Built target _ost_img_alg make -f modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/base/tests /<>/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 27%] running checks for module base cd /<>/modules/base/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_base_tests Running 5 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 27%] Built target ost_base_tests_run make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/src /<>/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 29%] Built target ost_bindings make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/base/tests /<>/obj-aarch64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 29%] running checks for module img cd /<>/modules/img/base/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_img_tests Running 44 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 29%] Built target ost_img_tests_run make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/tests /<>/obj-aarch64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 29%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -c /<>/modules/seq/base/tests/test_sequence.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_vec3.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_negate.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_negate.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_builder.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -c /<>/modules/mol/base/tests/test_builder.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/base/tests/test_sequence.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/base/tests/test_sequence.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -c /<>/modules/img/alg/tests/test_power_spectrum.cc [ 29%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -c /<>/modules/geom/tests/test_vec4.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /<>/modules/mol/base/tests/test_builder.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_vec4.cc:20: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_power_spectrum.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_power_spectrum.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -c /<>/modules/img/alg/tests/test_shift.cc [ 30%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -c /<>/modules/geom/tests/test_transform.cc [ 30%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_delete.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -c /<>/modules/mol/base/tests/test_delete.cc [ 30%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -c /<>/modules/seq/base/tests/test_aligned_column.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_shift.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_shift.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/modules/geom/tests/test_transform.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/geom/tests/test_transform.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_delete.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_delete.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -c /<>/modules/img/alg/tests/test_stat.cc [ 30%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -MF CMakeFiles/ost_geom_tests.dir/tests.cc.o.d -o CMakeFiles/ost_geom_tests.dir/tests.cc.o -c /<>/modules/geom/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/base/tests/test_aligned_column.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/base/tests/test_aligned_column.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/seq/base/tests/test_aligned_column.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/modules/seq/base/tests/test_aligned_column.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_entity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -c /<>/modules/mol/base/tests/test_entity.cc [ 31%] Linking CXX executable ../../../tests/ost_geom_tests cd /<>/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o CMakeFiles/ost_geom_tests.dir/tests.cc.o -o ../../../tests/ost_geom_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 31%] Built target ost_geom_tests make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/src /<>/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 32%] Built target ost_seq_alg make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod /<>/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 32%] Built target _ost_seq make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/src /<>/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/conop/src/CMakeFiles/ost_conop.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 33%] Built target ost_conop make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/db/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/db/pymod /<>/obj-aarch64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake "--color=" In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_stat.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_stat.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/db/pymod/CMakeFiles/_ost_db.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 33%] Built target _ost_db make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/src /<>/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 35%] Built target ost_mol_alg make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/bindings/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/bindings/pymod /<>/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 35%] Built target _ost_bindings make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/tests /<>/obj-aarch64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 35%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -c /<>/modules/conop/tests/test_amino_acids.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /<>/modules/mol/base/tests/test_entity.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_entity.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -c /<>/modules/seq/base/tests/test_aligned_region.cc /<>/modules/mol/base/tests/test_entity.cc: In member function ‘void mol_base::minmax::test_method()’: /<>/modules/mol/base/tests/test_entity.cc:438:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 438 | std::pair minmax = ev.GetMinMax("test", Prop::ATOM); | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /<>/modules/conop/tests/test_amino_acids.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/conop/tests/test_amino_acids.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -c /<>/modules/img/alg/tests/test_transform.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/base/tests/test_aligned_region.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/base/tests/test_aligned_region.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/seq/base/tests/test_aligned_region.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/modules/seq/base/tests/test_aligned_region.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_transform.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_transform.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -c /<>/modules/conop/tests/test_heuristic_conop.cc [ 35%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -c /<>/modules/img/alg/tests/test_normalizer.cc [ 35%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -c /<>/modules/seq/base/tests/test_alignment.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/conop/tests/test_heuristic_conop.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /<>/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /<>/modules/conop/tests/test_heuristic_conop.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/modules/img/alg/tests/test_normalizer.cc:35: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/modules/img/alg/tests/test_normalizer.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_ics.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -c /<>/modules/mol/base/tests/test_ics.cc [ 35%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -c /<>/modules/img/alg/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/seq/base/tests/test_alignment.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/base/tests/test_alignment.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/modules/seq/base/tests/test_alignment.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /<>/modules/seq/base/tests/test_alignment.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_ics.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_ics.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Linking CXX executable ../../../../tests/ost_img_alg_tests cd /<>/obj-aarch64-linux-gnu/modules/img/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_img_alg_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 35%] Built target ost_img_alg_tests make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/geom/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/geom/tests /<>/obj-aarch64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 35%] running checks for module geom cd /<>/modules/geom/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_geom_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 35%] Built target ost_geom_tests_run make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/img/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/img/alg/tests /<>/obj-aarch64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 36%] running checks for module img_alg cd /<>/modules/img/alg/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_img_alg_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 36%] Built target ost_img_alg_tests_run make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod /<>/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 37%] Built target _ost_seq_alg make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/src /<>/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/src/CMakeFiles/ost_gfx.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 44%] Built target ost_gfx make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/pymod /<>/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/conop/pymod/CMakeFiles/_ost_conop.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 45%] Built target _ost_conop make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/src /<>/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/io/src/CMakeFiles/ost_io.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 50%] Built target ost_io make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod /<>/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 51%] Built target _ost_mol_alg make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/tests /<>/obj-aarch64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 51%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o -MF CMakeFiles/ost_gfx_tests.dir/tests.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/tests.cc.o -c /<>/modules/gfx/tests/tests.cc [ 51%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -MF CMakeFiles/ost_conop_tests.dir/tests.cc.o.d -o CMakeFiles/ost_conop_tests.dir/tests.cc.o -c /<>/modules/conop/tests/tests.cc [ 51%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -c /<>/modules/gfx/tests/test_gfx_node.cc [ 51%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -c /<>/modules/conop/tests/test_rule_based_conop.cc [ 51%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_query.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_query.cc.o -c /<>/modules/mol/base/tests/test_query.cc [ 51%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_profile.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -c /<>/modules/seq/base/tests/test_profile.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /<>/modules/gfx/tests/test_gfx_node.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, from /<>/modules/gfx/tests/test_gfx_node.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/conop/tests/test_rule_based_conop.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/conop/tests/test_rule_based_conop.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/modules/mol/base/tests/test_query.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_query.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_tests.dir/tests.cc.o -c /<>/modules/seq/base/tests/tests.cc [ 52%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_color.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -c /<>/modules/gfx/tests/test_color.cc [ 52%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/helper.cc.o cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/helper.cc.o -MF CMakeFiles/ost_conop_tests.dir/helper.cc.o.d -o CMakeFiles/ost_conop_tests.dir/helper.cc.o -c /<>/modules/conop/tests/helper.cc In file included from /usr/include/c++/13/string:54: In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/string:42: In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/13/bits/basic_string.h:266:17: warning: ‘*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length’ may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In static member function ‘static constexpr void std::char_traits::assign(char_type&, const char_type&)’, inlined from ‘static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:428:23, inlined from ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:877:18, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/13/bits/char_traits.h:358:16: warning: ‘((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]’ may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ In member function ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’, inlined from ‘void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/variant.hpp:597:21, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from ‘typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]’ at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from ‘static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2338:48, inlined from ‘typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2350:43, inlined from ‘void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2081:41, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2108:27, inlined from ‘void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2095:10, inlined from ‘typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]’ at /usr/include/boost/variant/variant.hpp:2160:15, inlined from ‘void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ChainBase]’ at /<>/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from ‘ost::mol::EntityHandle make_query_test_entity()’ at /<>/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: ‘*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity’ may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function ‘ost::mol::EntityHandle make_query_test_entity()’: /usr/include/boost/variant/variant.hpp:2107:21: note: ‘temp’ declared here 2107 | variant temp(rhs); | ^~~~ [ 52%] Linking CXX executable ../../../../tests/ost_seq_tests cd /<>/obj-aarch64-linux-gnu/modules/seq/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o CMakeFiles/ost_seq_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /<>/modules/gfx/tests/test_color.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/iterator:61, from /usr/include/boost/operators.hpp:98, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 52%] Built target ost_seq_tests make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/tests /<>/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 52%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -MF CMakeFiles/ost_io_tests.dir/test_clustal.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -c /<>/modules/io/tests/test_clustal.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/conop/tests/helper.cc:3: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/conop/tests/helper.cc:2: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_surface.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -c /<>/modules/mol/base/tests/test_surface.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, from /<>/modules/io/tests/test_clustal.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_clustal.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /<>/modules/mol/base/tests/test_surface.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_surface.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o cd /<>/obj-aarch64-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -c /<>/modules/gfx/tests/test_map_octree.cc [ 52%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -c /<>/modules/io/tests/test_io_pdb.cc [ 52%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_residue.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -c /<>/modules/mol/base/tests/test_residue.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /<>/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, from /<>/modules/gfx/tests/test_map_octree.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_construct.h:61, from /usr/include/c++/13/bits/stl_tempbuf.h:61, from /usr/include/c++/13/memory:66, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /<>/modules/io/tests/test_io_pdb.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_pdb.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_residue.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_residue.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/io/tests/test_io_pdb.cc:33: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Linking CXX executable ../../../tests/ost_gfx_tests cd /<>/obj-aarch64-linux-gnu/modules/gfx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_gfx_tests.dir/tests.cc.o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -o ../../../tests/ost_gfx_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_gfx.so.2.5.0 ../../../stage/lib/libost_io.so.2.5.0 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 52%] Built target ost_gfx_tests make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 52%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -c /<>/modules/mol/alg/tests/test_superposition.cc [ 52%] Linking CXX executable ../../../tests/ost_conop_tests cd /<>/obj-aarch64-linux-gnu/modules/conop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o CMakeFiles/ost_conop_tests.dir/tests.cc.o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o CMakeFiles/ost_conop_tests.dir/helper.cc.o -o ../../../tests/ost_conop_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 52%] Built target ost_conop_tests make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/src /<>/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 53%] Built target ost_mol_mm make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/base/tests /<>/obj-aarch64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 53%] running checks for module seq cd /<>/modules/seq/base/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_seq_tests Running 32 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 53%] Built target ost_seq_tests_run make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 53%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -c /<>/modules/seq/alg/tests/test_distance_analysis.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /<>/modules/mol/alg/tests/test_superposition.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view.cc.o -c /<>/modules/mol/base/tests/test_view.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /<>/modules/seq/alg/tests/test_distance_analysis.cc:28: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/alg/tests/test_distance_analysis.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /<>/modules/seq/alg/tests/test_distance_analysis.cc:30: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26, from /<>/modules/seq/alg/tests/test_distance_analysis.cc:34: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function ‘std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const’: /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_view.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_view.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -c /<>/modules/mol/alg/tests/tests.cc [ 53%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -c /<>/modules/mol/alg/tests/test_consistency_checks.cc [ 53%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -c /<>/modules/mol/base/tests/test_transfer_connectivity.cc [ 53%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -c /<>/modules/seq/alg/tests/test_merge_pairwise_alignments.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/alg/tests/test_consistency_checks.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/alg/tests/test_consistency_checks.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /<>/modules/mol/base/tests/test_transfer_connectivity.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /<>/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -c /<>/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /<>/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /<>/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -c /<>/modules/mol/base/tests/test_view_op.cc [ 53%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -c /<>/modules/io/tests/test_io_crd.cc [ 54%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -c /<>/modules/seq/alg/tests/test_sequence_identity.cc [ 54%] Linking CXX executable ../../../../tests/ost_mol_alg_tests cd /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -o ../../../../tests/ost_mol_alg_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 54%] Built target ost_mol_alg_tests make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/pymod /<>/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 56%] Built target _ost_gfx make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/src /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/src /<>/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake "--color=" In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/mol/base/tests/test_view_op.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/base/tests/test_view_op.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/src/CMakeFiles/ost_gui.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 88%] Built target ost_gui make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/io/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/io/pymod /<>/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 89%] Built target _ost_io make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/conop/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/conop/tests /<>/obj-aarch64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 89%] running checks for module conop cd /<>/modules/conop/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_conop_tests Running 18 test cases... unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 89%] Built target ost_conop_tests_run [ 89%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, from /<>/modules/seq/alg/tests/test_sequence_identity.cc:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/seq/alg/tests/test_sequence_identity.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -c /<>/modules/seq/alg/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/io/tests/test_io_crd.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_crd.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gfx/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gfx/tests /<>/obj-aarch64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 90%] running checks for module gfx cd /<>/modules/gfx/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_gfx_tests [ 90%] Linking CXX executable ../../../../tests/ost_seq_alg_tests cd /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_alg_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 90%] Built target ost_seq_alg_tests make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests /<>/obj-aarch64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] running checks for module mol_alg cd /<>/modules/mol/alg/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_mol_alg_tests Running 4 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target ost_mol_alg_tests_run make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -c /<>/modules/mol/mm/tests/test_interaction.cc [ 91%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -c /<>/modules/io/tests/test_io_dcd.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/modules/mol/mm/tests/test_interaction.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_interaction.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, from /<>/modules/io/tests/test_io_dcd.cc:23: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_dcd.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_tests.dir/tests.cc.o -c /<>/modules/mol/base/tests/tests.cc [ 91%] Linking CXX executable ../../../../tests/ost_mol_tests cd /<>/obj-aarch64-linux-gnu/modules/mol/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o CMakeFiles/ost_mol_tests.dir/test_query.cc.o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o CMakeFiles/ost_mol_tests.dir/test_view.cc.o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o CMakeFiles/ost_mol_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target ost_mol_tests make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod /<>/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 92%] Built target _ost_mol_mm make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/seq/alg/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests /<>/obj-aarch64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 92%] running checks for module seq_alg cd /<>/modules/seq/alg/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_seq_alg_tests Running 19 test cases... *** No errors detected make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 92%] Built target ost_seq_alg_tests_run make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/gui/pymod /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/gui/pymod /<>/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake "--color=" [ 92%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -c /<>/modules/io/tests/test_io_sdf.cc make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/pymod/CMakeFiles/_ost_gui.dir/build'. make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 94%] Built target _ost_gui [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /<>/modules/io/tests/test_io_sequence_profile.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh:27, from /<>/modules/io/tests/test_io_sequence_profile.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_sequence_profile.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/io/tests/test_io_sdf.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_sdf.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -c /<>/modules/mol/mm/tests/test_block.cc [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -MF CMakeFiles/ost_io_tests.dir/test_pir.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /<>/modules/io/tests/test_pir.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/modules/mol/mm/tests/test_block.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_block.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -MF CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -c /<>/modules/io/tests/test_iomanager.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh:25, from /<>/modules/io/tests/test_pir.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_pir.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /<>/modules/io/tests/test_iomanager.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_iomanager.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -MF CMakeFiles/ost_io_tests.dir/tests.cc.o.d -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /<>/modules/io/tests/tests.cc [ 95%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -c /<>/modules/mol/mm/tests/test_block_modifiers.cc [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -MF CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /<>/modules/io/tests/test_star_parser.cc [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /<>/modules/io/tests/test_mmcif_reader.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /<>/modules/mol/mm/tests/test_block_modifiers.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_block_modifiers.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /<>/modules/io/tests/test_star_parser.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_star_parser.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /<>/modules/io/tests/test_mmcif_reader.cc:26: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_mmcif_reader.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -c /<>/modules/mol/mm/tests/test_topology.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /<>/modules/mol/mm/tests/test_topology.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_topology.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /<>/modules/mol/mm/tests/test_topology.cc:22: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /<>/modules/io/tests/test_mmcif_info.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /<>/modules/io/tests/test_mmcif_info.cc:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_mmcif_info.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_img.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /<>/modules/io/tests/test_io_img.cc [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -MF CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -c /<>/modules/io/tests/test_exceptions.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /<>/modules/io/tests/test_io_img.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_io_img.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /<>/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /<>/modules/io/tests/test_exceptions.cc:27: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/io/tests/test_exceptions.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -c /<>/modules/mol/mm/tests/test_forcefield.cc [ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -c /<>/modules/mol/mm/tests/test_simulation.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /<>/modules/mol/mm/tests/test_forcefield.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_forcefield.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Linking CXX executable ../../../tests/ost_io_tests cd /<>/obj-aarch64-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../stage/lib/libost_io.so.2.5.0 ../../../stage/lib/libost_mol_alg.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_img_alg.so.2.5.0 ../../../stage/lib/libost_img.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 96%] Built target ost_io_tests make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules/mol/base/tests /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/modules/mol/base/tests /<>/obj-aarch64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 96%] running checks for module mol cd /<>/modules/mol/base/tests && env OST_ROOT=/<>/obj-aarch64-linux-gnu/stage /<>/obj-aarch64-linux-gnu/tests/ost_mol_tests Running 72 test cases... ./modules/mol/base/tests/test_ics.cc(216): error: in "mol_base/ics_settorsion_linear_unbuffered": difference{4} between s.t2.GetAngle(){-2.3561945} and Real(3.14159265358979323846/4){0.785398185} exceeds 0.0001% *** 1 failure is detected in the test module "ost_mol_base" make[4]: *** [modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make:74: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run] Error 201 make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:5369: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/<>/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -c /<>/modules/mol/mm/tests/tests.cc In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /<>/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /<>/modules/mol/mm/tests/test_simulation.cc:21: /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tools/detail/print_helper.hpp:20, from /usr/include/boost/test/utils/lazy_ostream.hpp:16, from /usr/include/boost/test/tools/context.hpp:19, from /usr/include/boost/test/test_tools.hpp:42, from /usr/include/boost/test/unit_test.hpp:18, from /<>/modules/mol/mm/tests/test_simulation.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /<>/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /<>/modules/mol/mm/tests/test_simulation.cc:29: /<>/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Linking CXX executable ../../../../tests/ost_mol_mm_tests cd /<>/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/openstructure-2.5.0-1ubuntu1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-Bsymbolic-functions -Wl,-z,relro CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_mm_tests -L/<>/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/<>/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../../../stage/lib/libost_mol_mm.so.2.5.0 ../../../../stage/lib/libost_io.so.2.5.0 ../../../../stage/lib/libost_mol_alg.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../../stage/lib/libost_conop.so.2.5.0 ../../../../stage/lib/libost_db.so.2.5.0 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.83.0 ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.12 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.12 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libOpenMM.so make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 96%] Built target ost_mol_mm_tests E: Build killed with signal TERM after 150 minutes of inactivity -------------------------------------------------------------------------------- Build finished at 2024-04-03T17:23:40Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 2781400 Build-Time: 12116 Distribution: noble-proposed Fail-Stage: build Host Architecture: arm64 Install-Time: 158 Job: openstructure_2.5.0-1ubuntu1.dsc Machine Architecture: arm64 Package: openstructure Package-Time: 12283 Source-Version: 2.5.0-1ubuntu1 Space: 2781400 Status: attempted Version: 2.5.0-1ubuntu1 -------------------------------------------------------------------------------- Finished at 2024-04-03T17:23:40Z Build needed 03:24:43, 2781400k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27674365 Scanning for processes to kill in build PACKAGEBUILD-27674365