https://launchpad.net/ubuntu/+archive/test-rebuild-20240502-noble/+build/28177924 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-028 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:18 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~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... 13 May 07:15:16 ntpdate[1950]: adjust time server 10.211.37.1 offset -0.001575 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28177924 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-28177924 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28177924 Starting target for build PACKAGEBUILD-28177924 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28177924 'deb http://ftpmaster.internal/ubuntu noble main universe' Overriding sources.list in build-PACKAGEBUILD-28177924 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28177924 Updating target for build PACKAGEBUILD-28177924 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1377 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB] Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.3 MB] Get:5 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5982 kB] Fetched 23.4 MB in 4s (5210 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: advancecomp 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 findutils 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 libassuan0 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 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis 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 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 176 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 116 MB of archives. After this operation, 77.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1build1 [201 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3build3 [72.5 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3build3 [41.6 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1build1 [83.6 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-6ubuntu2 [141 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-6ubuntu2 [349 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-6ubuntu2 [85.6 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-6ubuntu2 [33.9 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.2-1build1 [17.0 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libapparmor1 arm64 4.0.0-beta3-0ubuntu3 [50.0 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-2build2 [14.8 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-2.1build1 [47.6 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu2 [30.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4build1 [118 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4build1 [85.9 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2build1 [472 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.6.1+really5.4.5-1 [125 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2build1 [271 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 31+20240202-2ubuntu7 [51.8 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblz4-1 arm64 1.9.4-1build1 [64.1 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu2 [212 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libselinux1 arm64 3.5-2ubuntu2 [79.9 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.3-9ubuntu6 [133 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [732 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6t64 arm64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4t64 arm64 1.23-5.1build1 [6578 B] Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.38t64 arm64 5.38.2-3.2build2 [4774 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 perl arm64 5.38.2-3.2build2 [231 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 perl-base arm64 5.38.2-3.2build2 [1777 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu5 [15.3 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-iconv-perl arm64 1.7-8build3 [13.1 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtext-charwidth-perl arm64 0.04-11build3 [9406 B] Get:39 http://ftpmaster.internal/ubuntu noble/universe arm64 libnss-nisplus arm64 1.3-5build1 [22.5 kB] Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 libnss-nis arm64 3.1-0ubuntu7 [26.6 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu8 [19.7 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu7 [64.8 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu8 [1596 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.39-0ubuntu8 [2774 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.39-0ubuntu8 [591 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 openssl arm64 3.0.13-0ubuntu3 [984 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd-shared arm64 255.4-1ubuntu8 [2016 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu4 [262 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3t64 arm64 3.0.13-0ubuntu3 [1793 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 systemd-sysv arm64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 systemd arm64 255.4-1ubuntu8 [3403 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libsystemd0 arm64 255.4-1ubuntu8 [424 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu5 [50.4 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.3-5ubuntu5 [278 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libnettle8t64 arm64 3.9.1-2.2build1 [192 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libhogweed6t64 arm64 3.9.1-2.2build1 [199 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu2 [276 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2build1 [530 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu3 [942 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libapt-pkg6.0t64 arm64 2.7.14build2 [935 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 bzip2 arm64 1.0.8-5.1 [34.0 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-1.0 arm64 1.0.8-5.1 [35.7 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-14-base arm64 14-20240412-0ubuntu1 [47.6 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-s1 arm64 14-20240412-0ubuntu1 [61.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++6 arm64 14-20240412-0ubuntu1 [748 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libudev1 arm64 255.4-1ubuntu8 [173 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2build1 [21.7 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu2 [61.7 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2ubuntu6 [243 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.6-1build1 [22.7 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2build1 [67.2 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libtasn1-6 arm64 4.19.0-3build1 [43.1 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu3 [11.3 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3build1 [51.1 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libassuan0 arm64 2.5.6-1build1 [36.8 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu2 [703 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 gpg arm64 2.4.4-2ubuntu17 [548 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8t64 arm64 8.2-4build1 [153 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-4build1 [56.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu2 [145 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu2 [104 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 gpg-agent arm64 2.4.4-2ubuntu17 [221 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 gpgconf arm64 2.4.4-2ubuntu17 [103 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu5 [34.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libnpth0t64 arm64 1.6-3.1build1 [8144 B] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 gpgv arm64 2.4.4-2ubuntu17 [150 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libseccomp2 arm64 2.5.5-1ubuntu3 [51.1 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 apt-utils arm64 2.7.14build2 [205 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 apt arm64 2.7.14build2 [1336 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.3-5ubuntu5 [67.8 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4build1 [20.5 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu3 [128 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-c5 arm64 0.17-1build1 [36.4 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.3-9ubuntu6 [35.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.3-9ubuntu6 [142 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.3-9ubuntu6 [116 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu4 [22.4 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-31.31 [1572 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu10 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.17build1 [90.2 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu4 [780 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.3-9ubuntu6 [97.7 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 coreutils arm64 9.4-3ubuntu6 [1363 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3build1 [248 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg arm64 1.22.6ubuntu6 [1265 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 dash arm64 0.5.12-6ubuntu5 [90.4 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1build1 [175 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 findutils arm64 4.9.0-5build1 [300 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4build1 [159 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu3 [97.2 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 hostname arm64 3.23+nmu2ubuntu2 [11.0 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu3 [200 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu2 [186 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2build1 [191 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.3-9ubuntu6 [1114 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu3 [33.8 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu4 [22.2 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu4 [225 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu4 [594 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 optipng arm64 0.7.8+ds-1build2 [109 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16t64 arm64 1.6.43-5build1 [185 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu6 [64.4 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.3-9ubuntu6 [32.5 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1build1 [11.0 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2build1 [24.6 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2build1 [291 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build5 [90.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu3 [839 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu3 [58.5 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu4 [16.5 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1build1 [124 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-2ubuntu1 [273 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.3-9ubuntu6 [71.5 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libgpm2 arm64 1.20.7-11 [14.7 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu2 [23.4 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 libjansson4 arm64 2.14-2build2 [34.4 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 psmisc arm64 23.7-1build1 [178 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.6.1+really5.4.5-1 [268 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 advancecomp arm64 2.5-1build1 [177 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-4ubuntu2 [777 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-4ubuntu2 [95.7 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-4ubuntu2 [99.8 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-4ubuntu2 [3291 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-4ubuntu2 [767 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-4ubuntu2 [18.1 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-4ubuntu2 [239 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-4ubuntu2 [14.4 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240412-0ubuntu1 [1155 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-23ubuntu4 [14.5 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu4 [2379 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240412-0ubuntu1 [27.9 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240412-0ubuntu1 [11.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240412-0ubuntu1 [2921 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240412-0ubuntu1 [1286 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240412-0ubuntu1 [1604 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-23ubuntu4 [472 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu4 [2470 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240412-0ubuntu1 [2692 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240412-0ubuntu1 [44.7 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-23ubuntu4 [1032 B] Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-23ubuntu4 [49.0 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3build1 [669 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main arm64 libmpfr6 arm64 4.2.1-1build1 [329 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1build1 [56.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [20.1 MB] Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [11.7 MB] Get:183 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [10.3 MB] Get:184 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:185 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:186 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:187 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:188 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:189 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:190 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:191 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:192 http://ftpmaster.internal/ubuntu noble/main arm64 patch arm64 2.7.6-7build3 [101 kB] Get:193 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build2 [178 kB] Get:194 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] Get:195 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:196 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Get:197 http://ftpmaster.internal/ubuntu noble/main arm64 liblockfile-bin arm64 1.17-1build3 [11.0 kB] Get:198 http://ftpmaster.internal/ubuntu noble/main arm64 liblockfile1 arm64 1.17-1build3 [6874 B] Get:199 http://ftpmaster.internal/ubuntu noble/main arm64 lockfile-progs arm64 0.1.19build2 [8440 B] Preconfiguring packages ... 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Unpacking libsystemd-shared:arm64 (255.4-1ubuntu8) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu4_arm64.deb ... Unpacking libcryptsetup12:arm64 (2:2.7.0-1ubuntu4) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15618 files and directories currently installed.) Removing libssl3:arm64 (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:arm64. (Reading database ... 15607 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_arm64.deb ... Unpacking libssl3t64:arm64 (3.0.13-0ubuntu3) ... Setting up libssl3t64:arm64 (3.0.13-0ubuntu3) ... (Reading database ... 15620 files and directories currently installed.) Preparing to unpack .../systemd-dev_255.4-1ubuntu8_all.deb ... Unpacking systemd-dev (255.4-1ubuntu8) over (253.5-1ubuntu6) ... 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Unpacking systemd (255.4-1ubuntu8) 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_255.4-1ubuntu8_arm64.deb ... 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Setting up cpp-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libgprofng0:arm64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:arm64 (8.2-4build1) ... Setting up libgcc-13-dev:arm64 (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:arm64 (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu4) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... 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 (13.2.0-23ubuntu4) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3build3) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up libnss-nisplus:arm64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:arm64 (3.1-0ubuntu7) ... 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 ... 15845 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-28177924 arm64 noble -c chroot:build-PACKAGEBUILD-28177924 --arch=arm64 --dist=noble --nolog gemmi_0.6.4+ds-1build1.dsc Initiating build PACKAGEBUILD-28177924 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:18 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-028.buildd +==============================================================================+ | gemmi 0.6.4+ds-1build1 (arm64) Mon, 13 May 2024 07:15:59 +0000 | +==============================================================================+ Package: gemmi Version: 0.6.4+ds-1build1 Source Version: 0.6.4+ds-1build1 Distribution: noble Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28177924/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-TQFXkx/resolver-Y0llSq' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemmi_0.6.4+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gemmi-TQFXkx/gemmi-0.6.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-TQFXkx' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev, 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [452 B] Get:5 copy:/<>/apt_archive ./ Packages [529 B] Fetched 1938 B in 0s (119 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 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 cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doctest-dev dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13t64 libblas3 libbrotli1 libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 libldap2 libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libstb-dev libstb0t64 libsub-override-perl libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types netbase po-debconf pybind11-dev python3 python3-dev python3-iniconfig python3-minimal python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pybind11 python3-pytest python3-setuptools python3.12 python3.12-dev python3.12-minimal tao-pegtl-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv gfortran python-setuptools-doc python3.12-venv python3.12-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libeigen3-dev python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doctest-dev dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13t64 libblas3 libbrotli1 libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 libldap2 libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libstb-dev libstb0t64 libsub-override-perl libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types netbase po-debconf pybind11-dev python3 python3-dev python3-iniconfig python3-minimal python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pybind11 python3-pytest python3-setuptools python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy tao-pegtl-dev zlib1g-dev 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 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Fetched 58.2 MB in 3s (20.1 MB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15845 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... 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_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up libexpat1:arm64 (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16163 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_arm64.deb ... 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Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up cmake-data (3.28.3-1build7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up doctest-dev (2.4.11-1) ... Setting up libstb0t64:arm64 (0.0~git20230129.5736b15+ds-1.2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:arm64 (2.6.7+dfsg-1~exp1ubuntu8) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:arm64 (3.12.0-3build1) ... 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 gettext (0.21-14ubuntu2) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libcurl4t64:arm64 (8.5.0-2ubuntu10) ... Setting up libtool (2.4.7-7build1) ... Setting up python3.12 (3.12.3-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libstb-dev:arm64 (0.0~git20230129.5736b15+ds-1.2) ... Setting up groff-base (1.23.0-3build2) ... Setting up libarchive13t64:arm64 (3.7.2-2) ... Setting up libpython3-stdlib:arm64 (3.12.3-0ubuntu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.12.3-0ubuntu1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up man-db (2.12.0-4build2) ... 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 python3-packaging (24.0-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up python3-pluggy (1.4.0-1) ... Setting up cmake (3.28.3-1build7) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:arm64 (3.12.3-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up python3-pytest (7.4.4-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-dev (3.12.3-0ubuntu1) ... Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20240401) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.4-1ubuntu8) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-181-generic #201-Ubuntu SMP Thu Mar 28 15:39:18 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13ubuntu10 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-aarch64-linux-gnu_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 cmake_3.28.3-1build7 cmake-data_3.28.3-1build7 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-aarch64-linux-gnu_13.2.0-23ubuntu4 cpp-aarch64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-python_6.20240401 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 doctest-dev_2.4.11-1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu4 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argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /<>/src/crd.cpp [ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /<>/src/ddl.cpp make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 8%] Built target options [ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -c /<>/src/eig3.cpp [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /<>/src/mmcif.cpp [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /<>/src/mmread_gz.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/src/mmread_gz.cpp:4: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 13%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -c /<>/src/mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/src/mtz.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 15%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /<>/src/mtz2cif.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/src/mtz2cif.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 15%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /<>/src/polyheur.cpp [ 17%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /<>/src/read_cif.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/src/read_cif.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 17%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /<>/src/resinfo.cpp [ 19%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /<>/src/riding_h.cpp [ 19%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /<>/src/sprintf.cpp /<>/src/sprintf.cpp:30:86: note: ‘#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.’ 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") | ^ [ 21%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /<>/src/to_mmcif.cpp [ 23%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /<>/src/to_pdb.cpp [ 23%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /<>/src/monlib.cpp [ 26%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /<>/src/topo.cpp [ 26%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /<>/src/xds_ascii.cpp In file included from /<>/include/gemmi/xds_ascii.hpp:11, from /<>/src/xds_ascii.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/include/gemmi/topo.hpp:8, from /<>/src/topo.cpp:3: In function ‘std::__copy_move::__copy_m(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’, inlined from ‘std::__copy_move_a2(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from ‘std::__copy_move_a1(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from ‘std::__copy_move_a > >, gemmi::Topo::Rule*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from ‘std::copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from ‘std::__uninitialized_copy::__uninit_copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, inlined from ‘std::uninitialized_copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘std::__uninitialized_copy_a > > >, gemmi::Topo::Rule*, gemmi::Topo::Rule>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*, std::allocator&)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector >::_M_range_insert > > > >(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::forward_iterator_tag)void’ at /usr/include/c++/13/bits/vector.tcc:814:38, inlined from ‘std::vector >::insert > > >, void>(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >)__gnu_cxx::__normal_iterator > >’ at /usr/include/c++/13/bits/stl_vector.h:1486:19, inlined from ‘gemmi::vector_move_extend(std::vector >&, std::vector >&&)void’ at /<>/include/gemmi/util.hpp:260:15, inlined from ‘gemmi::Topo::apply_all_restraints(gemmi::MonLib const&)’ at /<>/src/topo.cpp:594:27: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: ‘memmove’ writing between 17 and 9223372036854775792 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/stl_tree.h:64: In member function ‘std::__new_allocator::allocate(unsigned long, void const*)’, inlined from ‘std::allocator_traits >::allocate(std::allocator&, unsigned long)’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/13/bits/stl_vector.h:381:33, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/13/bits/stl_vector.h:378:7, inlined from ‘std::vector >::_M_range_insert > > > >(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::forward_iterator_tag)void’ at /usr/include/c++/13/bits/vector.tcc:805:40, inlined from ‘std::vector >::insert > > >, void>(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >)__gnu_cxx::__normal_iterator > >’ at /usr/include/c++/13/bits/stl_vector.h:1486:19, inlined from ‘gemmi::vector_move_extend(std::vector >&, std::vector >&&)void’ at /<>/include/gemmi/util.hpp:260:15, inlined from ‘gemmi::Topo::apply_all_restraints(gemmi::MonLib const&)’ at /<>/src/topo.cpp:594:27: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [16, 9223372036854775792] allocated by ‘operator new(unsigned long)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 28%] Linking CXX static library libgemmi_cpp.a /usr/bin/cmake -P CMakeFiles/gemmi_cpp.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libgemmi_cpp.a CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/ranlib libgemmi_cpp.a make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 28%] Built target gemmi_cpp make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.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" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 28%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -c /<>/prog/align.cpp [ 28%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /<>/python/gemmi.cpp [ 30%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden 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-Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /<>/python/align.cpp [ 34%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /<>/prog/cif2mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/cif2mtz.hpp:15, from /<>/prog/cif2mtz.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 36%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -c /<>/prog/cif2json.cpp [ 39%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -c /<>/prog/contact.cpp [ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /<>/python/ccp4.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/python/ccp4.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 39%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -c /<>/prog/contents.cpp [ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /<>/prog/convert.cpp [ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -MF CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -c /<>/python/chemcomp.cpp [ 45%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 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/<>/prog/diff.cpp [ 47%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -c /<>/prog/ecalc.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/ecalc.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 47%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /<>/prog/fprime.cpp [ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /<>/prog/grep.cpp [ 52%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -c /<>/prog/h.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/grep.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 52%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /<>/python/custom.cpp [ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/elem.cpp.o -MF CMakeFiles/gemmi_py.dir/python/elem.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/elem.cpp.o -c /<>/python/elem.cpp [ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/grid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/grid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/grid.cpp.o -c /<>/python/grid.cpp [ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /<>/prog/json2cif.cpp [ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /<>/prog/main.cpp [ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /<>/prog/map.cpp [ 58%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -c /<>/prog/map2sf.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/map.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/map2sf.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 60%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /<>/python/hkl.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/cif2mtz.hpp:15, from /<>/python/hkl.cpp:9: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /<>/prog/mapcoef.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/mapcoef.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 60%] Building CXX object CMakeFiles/gemmi_py.dir/python/meta.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /<>/python/meta.cpp [ 63%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /<>/prog/mask.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/mask.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 65%] Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -MF CMakeFiles/gemmi_py.dir/python/monlib.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -c /<>/python/monlib.cpp [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -c /<>/prog/merge.cpp [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -c /<>/prog/mondiff.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/merge.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 67%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden 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/<>/python/read.cpp In file included from /<>/include/gemmi/pdb.hpp:23, from /<>/python/read.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 71%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /<>/prog/mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/mtz.cpp:8: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 73%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /<>/python/recgrid.cpp [ 73%] Building CXX object CMakeFiles/gemmi_py.dir/python/scaling.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /<>/python/scaling.cpp [ 76%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /<>/prog/mtz2cif.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/prog/mtz2cif.cpp:8: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 78%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /<>/python/search.cpp [ 78%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /<>/python/sf.cpp [ 80%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /<>/python/sym.cpp In file included from /<>/include/gemmi/it92.hpp:16, from /<>/python/sf.cpp:6: /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/python/sf.cpp:60:36: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:83:20: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]’ /<>/python/sf.cpp:60:36: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:85:25: required from here /<>/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 1]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:128:32: required from ‘void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]’ /<>/python/sf.cpp:47:40: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:83:20: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o -c /<>/prog/prep.cpp [ 80%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /<>/python/topo.cpp [ 82%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /<>/python/unitcell.cpp [ 84%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /<>/python/write.cpp [ 86%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /<>/prog/reindex.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/reindex.cpp:9: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 86%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /<>/prog/residues.cpp [ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /<>/prog/rmsz.cpp [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /<>/prog/sf2map.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/sf2map.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /<>/prog/sfcalc.cpp [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /<>/prog/sg.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/sfcalc.cpp:9: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/it92.hpp:16, from /<>/prog/sfcalc.cpp:14: /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, float>; Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:122:32: required from ‘void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:196:11: required from ‘void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:201:5: required from ‘void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]’ /<>/prog/sfcalc.cpp:243:36: required from ‘void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]’ /<>/prog/sfcalc.cpp:690:23: required from ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]’ /<>/prog/sfcalc.cpp:812:43: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, double>; Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:122:32: required from ‘void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:196:11: required from ‘void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:201:5: required from ‘void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/prog/sfcalc.cpp:243:36: required from ‘void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::Neutron92; Real = float]’ /<>/prog/sfcalc.cpp:690:23: required from ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]’ /<>/prog/sfcalc.cpp:817:49: required from here /<>/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/prog/sfcalc.cpp:19: /<>/include/gemmi/dencalc.hpp: In function ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’: /<>/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 93%] Linking CXX shared module gemmi.cpython-312-aarch64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -shared -o gemmi.cpython-312-aarch64-linux-gnu.so CMakeFiles/gemmi_py.dir/python/mol.cpp.o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o CMakeFiles/gemmi_py.dir/python/align.cpp.o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o CMakeFiles/gemmi_py.dir/python/cif.cpp.o CMakeFiles/gemmi_py.dir/python/custom.cpp.o CMakeFiles/gemmi_py.dir/python/elem.cpp.o CMakeFiles/gemmi_py.dir/python/grid.cpp.o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o CMakeFiles/gemmi_py.dir/python/meta.cpp.o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o CMakeFiles/gemmi_py.dir/python/read.cpp.o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o CMakeFiles/gemmi_py.dir/python/search.cpp.o CMakeFiles/gemmi_py.dir/python/sf.cpp.o CMakeFiles/gemmi_py.dir/python/sym.cpp.o CMakeFiles/gemmi_py.dir/python/topo.cpp.o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o CMakeFiles/gemmi_py.dir/python/write.cpp.o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/lib/aarch64-linux-gnu/libz.so [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /<>/prog/tags.cpp [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /<>/prog/validate.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/tags.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/validate.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /<>/prog/validate_mon.cpp [ 97%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /<>/prog/wcn.cpp In file included from /<>/prog/wcn.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /<>/prog/xds2mtz.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/xds2mtz.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ /usr/src/gemmi-0.6.4+ds-1build1/include/gemmi/dencalc.hpp: In member function ‘calculate_with_derivative’: /usr/src/gemmi-0.6.4+ds-1build1/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_prog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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| ^ In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/docs/code/maybegz.cpp:2: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/merge.hpp:15, from /<>/tests/cif.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 87%] Linking CXX executable doc_newmtz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so [ 89%] Linking CXX executable check_conn /usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 89%] Built target doc_newmtz make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/test_disulf.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o /usr/bin/c++ -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /<>/tests/disulf.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/tests/disulf.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target check_conn make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] gemmi --version cd /<> && /<>/obj-aarch64-linux-gnu/gemmi --version gemmi 0.6.4 make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target print-version [ 91%] Building CXX object CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o -MF CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o -c /<>/src/mtz2cif.cpp [ 93%] Building CXX object CMakeFiles/cpptest.dir/src/eig3.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/eig3.cpp.o -MF CMakeFiles/cpptest.dir/src/eig3.cpp.o.d -o CMakeFiles/cpptest.dir/src/eig3.cpp.o -c /<>/src/eig3.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/src/mtz2cif.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 95%] Building CXX object CMakeFiles/cpptest.dir/src/sprintf.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/sprintf.cpp.o -MF CMakeFiles/cpptest.dir/src/sprintf.cpp.o.d -o CMakeFiles/cpptest.dir/src/sprintf.cpp.o -c /<>/src/sprintf.cpp [ 97%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o /usr/bin/c++ -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /<>/docs/code/mutate.cpp [ 97%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o CMakeFiles/cpptest.dir/src/eig3.cpp.o CMakeFiles/cpptest.dir/src/sprintf.cpp.o -o cpptest make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target cpptest [ 97%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target doc_maybegz [100%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target test_disulf make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/ctest -C None Test project /<>/obj-aarch64-linux-gnu Start 1: cpptest 1/1 Test #1: cpptest .......................... Passed 0.03 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.03 sec make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' PYTHONPATH=$(find . -name 'obj-*') pytest-3 -k 'not test_sfcalc_' ........................................................................ [ 38%] ............................s.................s......sssssssssssssss.... [ 76%] ............................................ [100%] =========================== short test summary info ============================ SKIPPED [1] tests/test_mol.py:535: BioPython not installed. SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. SKIPPED [1] tests/test_prog.py:121: Program gemmi not found. SKIPPED [1] tests/test_prog.py:130: Program gemmi not found. SKIPPED [1] tests/test_prog.py:139: Program gemmi not found. SKIPPED [1] tests/test_prog.py:47: Program gemmi not found. SKIPPED [1] tests/test_prog.py:55: Program gemmi not found. SKIPPED [1] tests/test_prog.py:62: Program gemmi not found. SKIPPED [1] tests/test_prog.py:68: Program gemmi not found. SKIPPED [1] tests/test_prog.py:74: Program gemmi not found. SKIPPED [1] tests/test_prog.py:80: Program gemmi not found. SKIPPED [1] tests/test_seq.py:127: BioPython not installed. SKIPPED [1] tests/test_seq.py:132: BioPython not installed. SKIPPED [1] tests/test_seq.py:139: BioPython not installed. SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 171 passed, 17 skipped, 2 deselected in 2.15s make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j4 install DESTDIR=/<>/gemmi-0.6.4\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" 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 preinstall make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/gemmi -- Installing: /<>/debian/tmp/usr/include/gemmi -- Installing: /<>/debian/tmp/usr/include/gemmi/merge.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/resinfo.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fileutil.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmread.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/refln.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/iterator.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/recgrid.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/model.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/neutron92.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/topo.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/addends.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/polyheur.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_chemcomp.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/qcp.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/floodfill.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/smcif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/atof.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/pirfasta.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/scaling.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/linkhunt.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/math.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmread_gz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/remarks.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/twin.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/monlib.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/formfact.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/metadata.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_json.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/seqalign.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/gz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/input.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mtz2cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/sprintf.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/dirwalk.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/xds_ascii.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/util.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/sfcalc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mtz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/version.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/asumask.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fstream.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/elem.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/seqid.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/modify.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/assembly.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/small.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/it92.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cellred.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/binner.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/riding_h.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmcif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/blob.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_pdb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/third_party -- Installing: /<>/debian/tmp/usr/include/gemmi/third_party/tinydir.h -- Installing: /<>/debian/tmp/usr/include/gemmi/third_party/sajson.h -- Installing: /<>/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /<>/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /<>/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/numb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/eig3.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/levmar.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/pdb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/enumstr.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/select.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/symmetry.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/calculate.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/pdb_id.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmdb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/stats.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/ddl.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/dencalc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/align.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/bond_idx.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/grid.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/seqtools.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/interop.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fail.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/unitcell.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/neighbor.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/read_map.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/reciproc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/json.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/bessel.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fourier.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/chemcomp.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/c4322.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/ecalc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/ccp4.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cif2mtz.hpp -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/libgemmi_cpp.a -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -- Installing: /<>/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so make[1]: Leaving directory '/<>/obj-aarch64-linux-gnu' dh_install -a -O--buildsystem=cmake dh_installdocs -a -O--buildsystem=cmake dh_installchangelogs -a -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/<>' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.6.4+ds --name 'CLI for GEMMI library' \ --no-info --help-option '' > debian/gemmi.1 sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1 sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1 dh_installman make[1]: Leaving directory '/<>' dh_python3 -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so: .debug_info section not present dh_strip -a -O--buildsystem=cmake e5ef1d55af47e5b8587e73d094eec57de374bb62 dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing gemmi (in debian/gemmi); do_strip: , oemstrip: pkgstriptranslations: processing gemmi-dev (in debian/gemmi-dev); do_strip: , oemstrip: pkgstriptranslations: processing python3-gemmi (in debian/python3-gemmi); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gemmi-dev/DEBIAN/control, package gemmi-dev, directory debian/gemmi-dev pkgstripfiles: processing control file: debian/gemmi/DEBIAN/control, package gemmi, directory debian/gemmi INFO: pkgstripfiles: waiting for lock (gemmi-dev) ... pkgstripfiles: Truncating usr/share/doc/gemmi/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemmi ... pkgstripfiles: processing control file: debian/python3-gemmi/DEBIAN/control, package python3-gemmi, directory debian/python3-gemmi pkgstripfiles: No PNG files. INFO: pkgstripfiles: waiting for lock (python3-gemmi) ... dpkg-deb: building package 'gemmi' in '../gemmi_0.6.4+ds-1build1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/gemmi-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemmi-dev ... INFO: pkgstripfiles: waiting for lock (python3-gemmi) ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.4+ds-1build1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/python3-gemmi/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-gemmi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.4+ds-1build1_arm64.deb'. dpkg-genbuildinfo --build=any -O../gemmi_0.6.4+ds-1build1_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../gemmi_0.6.4+ds-1build1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-13T07:23:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gemmi_0.6.4+ds-1build1_arm64.changes: ------------------------------------- Format: 1.8 Date: Fri, 19 Jan 2024 19:22:28 +0000 Source: gemmi Binary: gemmi gemmi-dev python3-gemmi Built-For-Profiles: noudeb Architecture: arm64 Version: 0.6.4+ds-1build1 Distribution: noble Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: gemmi - library for structural biology - executable gemmi-dev - library for structural biology python3-gemmi - library for structural biology - Python module Changes: gemmi (0.6.4+ds-1build1) noble; urgency=medium . * No-change rebuild with Python 3.12 as default Checksums-Sha1: ee764e87a3f205d39e5f48f02e683f23048f2e3e 1177044 gemmi-dev_0.6.4+ds-1build1_arm64.deb 7c285ae0491db3d4a721e6960ac399ead194efcf 8811 gemmi_0.6.4+ds-1build1_arm64.buildinfo 17698ec36214cb0ed914373779a48734f4f2b6a1 1020812 gemmi_0.6.4+ds-1build1_arm64.deb cc883d02ec9d3131990efd64f0bd2a7c6ad7c9b3 2126016 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha256: 3418503be0f6331f25bcb92ea567364d14759e859e76c4dd4a19cac2d75b46c7 1177044 gemmi-dev_0.6.4+ds-1build1_arm64.deb 4bdf388865eeb0af6a92a25875c5cdcf579fecf5275e3f8b9c6db63fcdb2d6a8 8811 gemmi_0.6.4+ds-1build1_arm64.buildinfo 25c739a15a2b2a7c1bd11653d63287686329bbb8b9477cf96e272aeea5c3c7a1 1020812 gemmi_0.6.4+ds-1build1_arm64.deb e9d71b4410e9b793f85555e7a8ca47a62e2e6c071eb3af028af75948be3f4035 2126016 python3-gemmi_0.6.4+ds-1build1_arm64.deb Files: 8320a391e5e3bed491187fbec04ae44f 1177044 libdevel optional gemmi-dev_0.6.4+ds-1build1_arm64.deb d2e3173e6731668caecb35594dd1d424 8811 science optional gemmi_0.6.4+ds-1build1_arm64.buildinfo 8584f309242c243c51f4111bc783c939 1020812 science optional gemmi_0.6.4+ds-1build1_arm64.deb 1956c0c70c30b83c78beb2378c6840ea 2126016 python optional python3-gemmi_0.6.4+ds-1build1_arm64.deb /<>/gemmi_0.6.4+ds-1build1_arm64.changes.new could not be renamed to /<>/gemmi_0.6.4+ds-1build1_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: gemmi Binary: gemmi gemmi-dev python3-gemmi Architecture: arm64 Version: 0.6.4+ds-1build1 Checksums-Md5: 8320a391e5e3bed491187fbec04ae44f 1177044 gemmi-dev_0.6.4+ds-1build1_arm64.deb 8584f309242c243c51f4111bc783c939 1020812 gemmi_0.6.4+ds-1build1_arm64.deb 1956c0c70c30b83c78beb2378c6840ea 2126016 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha1: ee764e87a3f205d39e5f48f02e683f23048f2e3e 1177044 gemmi-dev_0.6.4+ds-1build1_arm64.deb 17698ec36214cb0ed914373779a48734f4f2b6a1 1020812 gemmi_0.6.4+ds-1build1_arm64.deb cc883d02ec9d3131990efd64f0bd2a7c6ad7c9b3 2126016 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha256: 3418503be0f6331f25bcb92ea567364d14759e859e76c4dd4a19cac2d75b46c7 1177044 gemmi-dev_0.6.4+ds-1build1_arm64.deb 25c739a15a2b2a7c1bd11653d63287686329bbb8b9477cf96e272aeea5c3c7a1 1020812 gemmi_0.6.4+ds-1build1_arm64.deb e9d71b4410e9b793f85555e7a8ca47a62e2e6c071eb3af028af75948be3f4035 2126016 python3-gemmi_0.6.4+ds-1build1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Mon, 13 May 2024 07:23:09 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu2), autotools-dev (= 20220109.1), base-files (= 13ubuntu10), base-passwd (= 3.6.3build1), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-aarch64-linux-gnu (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu6), bsdutils (= 1:2.39.3-9ubuntu6), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), cmake (= 3.28.3-1build7), cmake-data (= 3.28.3-1build7), coreutils (= 9.4-3ubuntu6), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu4), cpp-13-aarch64-linux-gnu (= 13.2.0-23ubuntu4), cpp-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86ubuntu1), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build2), dh-autoreconf (= 20), dh-python (= 6.20240401), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1build1), doctest-dev (= 2.4.11-1), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5build1), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu4), g++-13-aarch64-linux-gnu (= 13.2.0-23ubuntu4), g++-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu4), gcc-13-aarch64-linux-gnu (= 13.2.0-23ubuntu4), gcc-13-base (= 13.2.0-23ubuntu4), gcc-14-base (= 14-20240412-0ubuntu1), gcc-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu2), gettext-base (= 0.21-14ubuntu2), grep (= 3.11-4build1), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu3), help2man (= 1.49.3), hostname (= 3.23+nmu2ubuntu2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1build1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.2-2), libasan8 (= 14-20240412-0ubuntu1), libatomic1 (= 14-20240412-0ubuntu1), libattr1 (= 1:2.5.2-1build1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblas3 (= 3.12.0-3build1), libblkid1 (= 2.39.3-9ubuntu6), libbrotli1 (= 1.1.0-2build2), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu2), libcc1-0 (= 14-20240412-0ubuntu1), libcom-err2 (= 1.47.0-2.4~exp1ubuntu4), libcrypt-dev (= 1:4.4.36-4build1), libcrypt1 (= 1:4.4.36-4build1), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl4t64 (= 8.5.0-2ubuntu10), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build4), libelf1t64 (= 0.190-1.1build4), libexpat1 (= 2.6.1-2build1), libexpat1-dev (= 2.6.1-2build1), libffi8 (= 3.4.6-1build1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu4), libgcc-s1 (= 14-20240412-0ubuntu1), libgcrypt20 (= 1.10.3-2build1), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran5 (= 14-20240412-0ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu6), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240412-0ubuntu1), libgpg-error0 (= 1.47-3build2), libgprofng0 (= 2.42-4ubuntu2), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libhogweed6t64 (= 3.9.1-2.2build1), libhwasan0 (= 14-20240412-0ubuntu1), libicu74 (= 74.2-1ubuntu3), libidn2-0 (= 2.3.7-2build1), libisl23 (= 0.26-3build1), libitm1 (= 14-20240412-0ubuntu1), libjansson4 (= 2.14-2build2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 7.2.6-6), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjsoncpp25 (= 1.9.5-6build1), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3build1), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblapack3 (= 3.12.0-3build1), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu8), liblocale-gettext-perl (= 1.07-6ubuntu5), liblsan0 (= 14-20240412-0ubuntu1), liblz4-1 (= 1.9.4-1build1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2build1), libmount1 (= 2.39.3-9ubuntu6), libmpc3 (= 1.3.1-1build1), libmpfr6 (= 4.2.1-1build1), libncursesw6 (= 6.4+20240113-1ubuntu2), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build4), libp11-kit0 (= 0.25.3-4ubuntu2), libpam-modules (= 1.5.3-5ubuntu5), libpam-modules-bin (= 1.5.3-5ubuntu5), libpam-runtime (= 1.5.3-5ubuntu5), libpam0g (= 1.5.3-5ubuntu5), libpcre2-8-0 (= 10.42-4ubuntu2), libperl5.38t64 (= 5.38.2-3.2build2), libpipeline1 (= 1.5.7-2), libproc2-0 (= 2:4.0.4-4ubuntu3), libpsl5t64 (= 0.21.2-1.1build1), libpython3-dev (= 3.12.3-0ubuntu1), libpython3-stdlib (= 3.12.3-0ubuntu1), libpython3.12-dev (= 3.12.3-1), libpython3.12-minimal (= 3.12.3-1), libpython3.12-stdlib (= 3.12.3-1), libpython3.12t64 (= 3.12.3-1), libreadline8t64 (= 8.2-4build1), librhash0 (= 1.4.3-3build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu3), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu3), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu6), libsqlite3-0 (= 3.45.1-1ubuntu2), libssh-4 (= 0.10.6-2build2), libssl3t64 (= 3.0.13-0ubuntu3), libstb-dev (= 0.0~git20230129.5736b15+ds-1.2), libstb0t64 (= 0.0~git20230129.5736b15+ds-1.2), libstdc++-13-dev (= 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SOURCE_DATE_EPOCH="1705692148" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gemmi-dev_0.6.4+ds-1build1_arm64.deb ------------------------------------ new Debian package, version 2.0. size 1177044 bytes: control archive=3541 bytes. 820 bytes, 19 lines control 7165 bytes, 110 lines md5sums Package: gemmi-dev Source: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 5937 Section: libdevel Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains header-only C++ library. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/include/gemmi/ -rw-r--r-- root/root 844 2023-12-13 10:39 ./usr/include/gemmi/addends.hpp -rw-r--r-- root/root 11686 2023-12-13 10:39 ./usr/include/gemmi/align.hpp -rw-r--r-- root/root 4460 2023-12-13 10:39 ./usr/include/gemmi/assembly.hpp -rw-r--r-- root/root 7455 2023-12-13 10:39 ./usr/include/gemmi/asudata.hpp -rw-r--r-- root/root 11452 2023-12-13 10:39 ./usr/include/gemmi/asumask.hpp -rw-r--r-- root/root 1023 2023-12-13 10:39 ./usr/include/gemmi/atof.hpp -rw-r--r-- root/root 3810 2023-12-13 10:39 ./usr/include/gemmi/atox.hpp -rw-r--r-- root/root 3983 2023-12-13 10:39 ./usr/include/gemmi/bessel.hpp -rw-r--r-- root/root 7728 2023-12-13 10:39 ./usr/include/gemmi/binner.hpp -rw-r--r-- root/root 4864 2023-12-13 10:39 ./usr/include/gemmi/blob.hpp 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./usr/include/gemmi/grid.hpp -rw-r--r-- root/root 5164 2023-12-13 10:39 ./usr/include/gemmi/gz.hpp -rw-r--r-- root/root 4512 2023-12-13 10:39 ./usr/include/gemmi/input.hpp -rw-r--r-- root/root 1864 2023-12-13 10:39 ./usr/include/gemmi/interop.hpp -rw-r--r-- root/root 23738 2023-12-13 10:39 ./usr/include/gemmi/it92.hpp -rw-r--r-- root/root 10089 2023-12-13 10:39 ./usr/include/gemmi/iterator.hpp -rw-r--r-- root/root 4820 2023-12-13 10:39 ./usr/include/gemmi/json.hpp -rw-r--r-- root/root 9023 2023-12-13 10:39 ./usr/include/gemmi/levmar.hpp -rw-r--r-- root/root 6763 2023-12-13 10:39 ./usr/include/gemmi/linkhunt.hpp -rw-r--r-- root/root 15168 2023-12-13 10:39 ./usr/include/gemmi/math.hpp -rw-r--r-- root/root 16861 2023-12-13 10:39 ./usr/include/gemmi/merge.hpp -rw-r--r-- root/root 13775 2023-12-13 10:39 ./usr/include/gemmi/metadata.hpp -rw-r--r-- root/root 991 2023-12-13 10:39 ./usr/include/gemmi/mmcif.hpp -rw-r--r-- root/root 1200 2023-12-13 10:39 ./usr/include/gemmi/mmcif_impl.hpp 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2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/gemmi-dev/ -rw-r--r-- root/root 802 2024-01-19 19:22 ./usr/share/doc/gemmi-dev/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/gemmi-dev/copyright gemmi_0.6.4+ds-1build1_arm64.deb -------------------------------- new Debian package, version 2.0. size 1020812 bytes: control archive=847 bytes. 900 bytes, 19 lines control 250 bytes, 4 lines md5sums Package: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 2267 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology - executable Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains main gemmi executable. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/bin/ -rwxr-xr-x root/root 2301200 2024-01-19 19:22 ./usr/bin/gemmi drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/gemmi/ -rw-r--r-- root/root 799 2024-01-19 19:22 ./usr/share/doc/gemmi/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/gemmi/copyright drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/man/man1/ -rw-r--r-- root/root 885 2024-01-19 19:22 ./usr/share/man/man1/gemmi.1.gz python3-gemmi_0.6.4+ds-1build1_arm64.deb ---------------------------------------- new Debian package, version 2.0. size 2126016 bytes: control archive=879 bytes. 959 bytes, 20 lines control 257 bytes, 3 lines md5sums Package: python3-gemmi Source: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 6984 Depends: python3 (<< 3.13), python3 (>= 3.12~), libc6 (>= 2.38), libgcc-s1 (>= 4.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6) Section: python Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology - Python module Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains the Python module. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 7132968 2024-01-19 19:22 ./usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/python3-gemmi/ -rw-r--r-- root/root 804 2024-01-19 19:22 ./usr/share/doc/python3-gemmi/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/python3-gemmi/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 1390928 Build-Time: 412 Distribution: noble Host Architecture: arm64 Install-Time: 18 Job: gemmi_0.6.4+ds-1build1.dsc Machine Architecture: arm64 Package: gemmi Package-Time: 430 Source-Version: 0.6.4+ds-1build1 Space: 1390928 Status: successful Version: 0.6.4+ds-1build1 -------------------------------------------------------------------------------- Finished at 2024-05-13T07:23:09Z Build needed 00:07:10, 1390928k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28177924 Scanning for processes to kill in build PACKAGEBUILD-28177924