https://launchpad.net/ubuntu/+source/shasta/0.11.1-4build2/+build/27851044 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-002 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 12 Mar 11:31:07 ntpdate[1860]: adjust time server 10.211.37.1 offset 0.009679 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27851044 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27851044 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27851044 Starting target for build PACKAGEBUILD-27851044 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27851044 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27851044 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27851044 Updating target for build PACKAGEBUILD-27851044 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1417 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6039 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [600 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [211 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3227 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1187 kB] Fetched 28.7 MB in 6s (4432 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* libcom-err2* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libreadline8* libss2* 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 libcom-err2t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libreadline8t64 libss2t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: optipng The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 155 upgraded, 24 newly installed, 15 to remove and 1 not upgraded. Need to get 114 MB of archives. After this operation, 77.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl-dev arm64 1.3.0-3build2 [72.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu5 [1596 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu5 [19.7 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnss-nisplus arm64 1.3-5 [22.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgssapi-krb5-2 arm64 1.20.1-5.1build2 [141 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5-3 arm64 1.20.1-5.1build2 [349 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libk5crypto3 arm64 1.20.1-5.1build2 [85.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5support0 arm64 1.20.1-5.1build2 [33.8 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcom-err2t64 arm64 1.47.0-2.3ubuntu1 [22.2 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libext2fs2t64 arm64 1.47.0-2.3ubuntu1 [214 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 logsave arm64 1.47.0-2.3ubuntu1 [21.9 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libss2t64 arm64 1.47.0-2.3ubuntu1 [16.6 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 e2fsprogs arm64 1.47.0-2.3ubuntu1 [592 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.2-1 [17.0 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapparmor1 arm64 4.0.0~beta2-0ubuntu3 [49.7 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit-common all 1:3.1.2-2.1 [5674 B] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-2 [14.7 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit1 arm64 1:3.1.2-2.1 [47.5 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libblkid1 arm64 2.39.3-9ubuntu2 [122 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu1 [30.1 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblzma5 arm64 5.6.0-0.2 [129 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkmod2 arm64 31+20240202-2ubuntu4 [51.6 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libselinux1 arm64 3.5-2build2 [79.5 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmount1 arm64 2.39.3-9ubuntu2 [133 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu3 [15.2 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build2 [13.1 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-charwidth-perl arm64 0.04-11build2 [9368 B] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6 arm64 2.39-0ubuntu5 [2775 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-bin arm64 2.39-0ubuntu5 [591 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.4-1ubuntu4 [2015 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu2 [262 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.4-1ubuntu4 [103 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.4-1ubuntu4 [11.9 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.4-1ubuntu4 [3403 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.4-1ubuntu4 [424 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu3 [50.4 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules arm64 1.5.3-5ubuntu3 [278 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2 [192 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2 [199 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu1 [275 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu2 [1042 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapt-pkg6.0t64 arm64 2.7.13ubuntu1 [933 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 bzip2 arm64 1.0.8-5ubuntu1 [34.0 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-1.0 arm64 1.0.8-5ubuntu1 [35.8 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-14-base arm64 14-20240303-1ubuntu1 [46.9 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-s1 arm64 14-20240303-1ubuntu1 [49.9 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++6 arm64 14-20240303-1ubuntu1 [749 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.4-1ubuntu4 [173 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu1 [61.7 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.6-1 [22.6 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2 [67.1 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebconfclient0 arm64 0.271ubuntu2 [11.2 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu1 [704 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg arm64 2.4.4-2ubuntu15 [548 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu1 [146 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu1 [104 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg-agent arm64 2.4.4-2ubuntu15 [221 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgconf arm64 2.4.4-2ubuntu15 [103 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 pinentry-curses arm64 1.2.1-3ubuntu3 [34.2 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libnpth0t64 arm64 1.6-3.1 [8076 B] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgv arm64 2.4.4-2ubuntu15 [150 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libseccomp2 arm64 2.5.5-1ubuntu1 [51.0 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt-utils arm64 2.7.13ubuntu1 [205 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt arm64 2.7.13ubuntu1 [1335 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 debconf-i18n all 1.5.86 [205 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 debconf all 1.5.86 [124 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam0g arm64 1.5.3-5ubuntu3 [67.7 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu2 [128 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libuuid1 arm64 2.39.3-9ubuntu2 [35.1 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfdisk1 arm64 2.39.3-9ubuntu2 [142 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 mount arm64 2.39.3-9ubuntu2 [116 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3 [9550 B] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl2 arm64 1.3.0-3build2 [41.5 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu7 [74.4 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debianutils arm64 5.17 [90.1 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu2 [780 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdutils arm64 1:2.39.3-9ubuntu2 [97.4 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 coreutils arm64 9.4-3ubuntu3 [1363 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.5ubuntu4 [1267 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 dash arm64 0.5.12-6ubuntu4 [90.3 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu2 [97.1 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 hostname arm64 3.23+nmu2ubuntu1 [10.9 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu1 [200 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu1 [186 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 util-linux arm64 2.39.3-9ubuntu2 [1114 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu2 [33.8 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu2 [64.1 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 uuid-runtime arm64 2.39.3-9ubuntu2 [32.5 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage-common all 3.5-1build3 [10.1 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage2 arm64 3.5-1build3 [90.7 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu1 [838 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-3ubuntu1 [777 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-3ubuntu1 [95.7 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-3ubuntu1 [99.9 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-3ubuntu1 [14.5 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-3ubuntu1 [3292 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-3ubuntu1 [767 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-3ubuntu1 [18.0 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-3ubuntu1 [239 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-17ubuntu2 [47.4 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu1 [58.4 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1 [124 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-4ubuntu1 [708 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 krb5-locales all 1.20.1-5.1build2 [13.8 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu1 [23.3 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-1ubuntu1 [273 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdextrautils arm64 2.39.3-9ubuntu2 [71.5 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16 arm64 1.6.43-1 [184 kB] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.7-1 [178 kB] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 xz-utils arm64 5.6.0-0.2 [272 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:170 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:171 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.5ubuntu4 [1060 kB] Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.5ubuntu4 [269 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Preconfiguring packages ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27851044 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27851044 --arch=arm64 --dist=noble-proposed --nolog shasta_0.11.1-4build2.dsc Initiating build PACKAGEBUILD-27851044 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-002.buildd +==============================================================================+ | shasta 0.11.1-4build2 (arm64) Tue, 12 Mar 2024 11:32:59 +0000 | +==============================================================================+ Package: shasta Version: 0.11.1-4build2 Source Version: 0.11.1-4build2 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27851044/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/shasta-ew9T5Q/resolver-ANWJqj' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- shasta_0.11.1-4build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/shasta-ew9T5Q/shasta-0.11.1' with '<>' I: NOTICE: Log filtering will replace 'build/shasta-ew9T5Q' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcereal-dev, libblas-dev, liblapack-dev, gfortran, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-exec, cmake, patchelf, chrpath, libboost-all-dev, libpng-dev, ncbi-blast+, python3-dev, python3-sphinx, libpython3-dev, libseqan2-dev, libspoa-dev, python3-pybind11, libcereal-dev, libblas-dev, liblapack-dev, gfortran, 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 [501 B] Get:5 copy:/<>/apt_archive ./ Packages [564 B] Fetched 2022 B in 0s (36.5 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 debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 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 chrpath cmake cmake-data debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcereal-dev libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm17t64 liblmdb0 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpng-dev libpng16-16t64 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libspoa-dev libspoa7.0.0 libssh-4 libsub-override-perl libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-bin mpi-default-dev ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client patchelf po-debconf pybind11-dev python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-dev python3-docutils python3-idna python3-imagesize python3-jinja2 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-tz python3-urllib3 python3.12 python3.12-dev python3.12-minimal rapidjson-dev sgml-base sphinx-common xml-core 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 gfortran-doc gfortran-13-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc graphviz libboost1.83-doc gccxml libboost-contract1.83-dev libmpfrc++-dev libntl-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-stemmer dvipng fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax python3-lib2to3 python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.12-venv python3.12-doc binfmt-support rapidjson-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl libldap-common libcoarrays-openmpi-dev libpng-tools publicsuffix libsasl2-modules xauth libmail-sendmail-perl libeigen3-dev libpaper-utils python3-pil python3-numpy The following packages will be REMOVED: libpng16-16* The following NEW packages will be installed: autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-all-dev libboost-atomic-dev libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono-dev libboost-chrono1.83-dev libboost-chrono1.83.0t64 libboost-container-dev libboost-container1.83-dev libboost-container1.83.0 libboost-context-dev libboost-context1.83-dev libboost-context1.83.0 libboost-coroutine-dev libboost-coroutine1.83-dev libboost-coroutine1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-dev libboost-exception-dev libboost-exception1.83-dev libboost-fiber-dev libboost-fiber1.83-dev libboost-fiber1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-graph-dev libboost-graph-parallel-dev libboost-graph-parallel1.83-dev libboost-graph-parallel1.83.0 libboost-graph1.83-dev libboost-graph1.83.0 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-json-dev libboost-json1.83-dev libboost-json1.83.0 libboost-locale-dev libboost-locale1.83-dev libboost-locale1.83.0 libboost-log-dev libboost-log1.83-dev libboost-log1.83.0 libboost-math-dev libboost-math1.83-dev libboost-math1.83.0 libboost-mpi-dev libboost-mpi-python-dev libboost-mpi-python1.83-dev libboost-mpi-python1.83.0 libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-nowide-dev libboost-nowide1.83-dev libboost-nowide1.83.0 libboost-numpy-dev libboost-numpy1.83-dev libboost-numpy1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-random-dev libboost-random1.83-dev libboost-random1.83.0 libboost-regex-dev libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-stacktrace-dev libboost-stacktrace1.83-dev libboost-stacktrace1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-test-dev libboost-test1.83-dev libboost-test1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-timer-dev libboost-timer1.83-dev libboost-timer1.83.0 libboost-tools-dev libboost-type-erasure-dev libboost-type-erasure1.83-dev libboost-type-erasure1.83.0 libboost-url-dev libboost-url1.83-dev libboost-url1.83.0 libboost-wave-dev libboost-wave1.83-dev libboost-wave1.83.0 libboost1.83-dev libboost1.83-tools-dev libbrotli1 libbsd0 libcbor0.10 libcereal-dev libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm17t64 liblmdb0 libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libpng-dev libpng16-16t64 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librdmacm1t64 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libspoa-dev libspoa7.0.0 libssh-4 libsub-override-perl libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-bin mpi-default-dev ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client patchelf po-debconf pybind11-dev python-babel-localedata python3 python3-alabaster python3-babel python3-certifi python3-chardet python3-dev python3-docutils python3-idna python3-imagesize python3-jinja2 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-tz python3-urllib3 python3.12 python3.12-dev python3.12-minimal rapidjson-dev sbuild-build-depends-main-dummy sgml-base sphinx-common xml-core zlib1g-dev 0 upgraded, 280 newly installed, 1 to remove and 1 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [782 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-minimal arm64 3.12.2-4build2 [829 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libexpat1 arm64 2.6.1-2 [76.0 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12-minimal arm64 3.12.2-4build2 [2189 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-minimal arm64 3.12.2-0ubuntu1 [27.1 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 media-types all 10.1.0 [27.5 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 netbase all 6.4 [13.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-stdlib arm64 3.12.2-4build2 [2002 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12 arm64 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noble/main arm64 liblmdb0 arm64 0.9.31-1 [47.4 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnghttp2-14 arm64 1.59.0-1build1 [74.0 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpipeline1 arm64 1.5.7-1 [23.3 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libxau6 arm64 1:1.0.9-1build5 [7624 B] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu5 [10.8 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb1 arm64 1.15-1 [47.6 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-data all 2:1.8.7-1 [115 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-6 arm64 2:1.8.7-1 [645 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxext6 arm64 2:1.3.4-1build1 [31.1 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 man-db arm64 2.12.0-3build4 [1226 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssh-client arm64 1:9.6p1-3ubuntu7 [883 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 chrpath arm64 0.16-2build1 [12.5 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libarchive13t64 arm64 3.7.2-1.1ubuntu1 [376 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libbrotli1 arm64 1.1.0-2 [339 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4ubuntu4 [21.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4ubuntu4 [54.7 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libldap2 arm64 2.6.7+dfsg-1~exp1ubuntu6 [193 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build6 [57.8 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssh-4 arm64 0.10.6-2build1 [190 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4 arm64 8.5.0-2ubuntu6 [332 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libjsoncpp25 arm64 1.9.5-6 [76.0 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 librhash0 arm64 1.4.3-3 [125 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libuv1t64 arm64 1.48.0-1.1 [95.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cmake-data all 3.28.3-1build3 [2155 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cmake arm64 3.28.3-1build3 [10.3 MB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libelf1t64 arm64 0.190-1.1build1 [57.9 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdw1t64 arm64 0.190-1.1build1 [258 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debugedit arm64 1:5.0-5build1 [45.4 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dwz arm64 0.15-1build5 [113 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 gettext arm64 0.21-14ubuntu1 [846 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debhelper all 13.14.1ubuntu5 [869 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 dh-python all 6.20231223ubuntu2 [111 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 docutils-common all 0.20.1+dfsg-3 [132 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-200 arm64 3.7.0-0.3 [57.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [182 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libibverbs1 arm64 50.0-2build1 [67.3 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ibverbs-providers arm64 50.0-2build1 [367 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libllvm17t64 arm64 1:17.0.6-8ubuntu1.1 [25.0 MB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build1 [14.1 MB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libhsakmt1 arm64 5.7.0-1 [63.6 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhsa-runtime64-1 arm64 5.7.1-1build1 [286 kB] Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 libamdhip64-5 arm64 5.2.3-12 [5134 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost1.83-dev arm64 1.83.0-2.1ubuntu1 [10.7 MB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-dev arm64 1.83.0.1ubuntu2 [4308 B] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost1.83-tools-dev arm64 1.83.0-2.1ubuntu1 [1362 kB] Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-tools-dev arm64 1.83.0.1ubuntu2 [4238 B] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-atomic1.83.0 arm64 1.83.0-2.1ubuntu1 [239 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-atomic1.83-dev arm64 1.83.0-2.1ubuntu1 [235 kB] Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-atomic-dev arm64 1.83.0.1ubuntu2 [4358 B] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-2.1ubuntu1 [244 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-chrono1.83-dev arm64 1.83.0-2.1ubuntu1 [245 kB] Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-chrono-dev arm64 1.83.0.1ubuntu2 [4672 B] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-container1.83.0 arm64 1.83.0-2.1ubuntu1 [261 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-container1.83-dev arm64 1.83.0-2.1ubuntu1 [270 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-container-dev arm64 1.83.0.1ubuntu2 [4530 B] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-date-time1.83.0 arm64 1.83.0-2.1ubuntu1 [236 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-serialization1.83.0 arm64 1.83.0-2.1ubuntu1 [335 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-serialization1.83-dev arm64 1.83.0-2.1ubuntu1 [392 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-date-time1.83-dev arm64 1.83.0-2.1ubuntu1 [239 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-system1.83.0 arm64 1.83.0-2.1ubuntu1 [236 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-system1.83-dev arm64 1.83.0-2.1ubuntu1 [231 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-thread1.83.0 arm64 1.83.0-2.1ubuntu1 [275 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-thread1.83-dev arm64 1.83.0-2.1ubuntu1 [284 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-context1.83.0 arm64 1.83.0-2.1ubuntu1 [237 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-context1.83-dev arm64 1.83.0-2.1ubuntu1 [232 kB] Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-context-dev arm64 1.83.0.1ubuntu2 [4276 B] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-coroutine1.83.0 arm64 1.83.0-2.1ubuntu1 [234 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-coroutine1.83-dev arm64 1.83.0-2.1ubuntu1 [237 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-coroutine-dev arm64 1.83.0.1ubuntu2 [4342 B] Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-date-time-dev arm64 1.83.0.1ubuntu2 [4058 B] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-exception1.83-dev arm64 1.83.0-2.1ubuntu1 [230 kB] Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-exception-dev arm64 1.83.0.1ubuntu2 [4058 B] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-2.1ubuntu1 [281 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-filesystem1.83-dev arm64 1.83.0-2.1ubuntu1 [301 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-fiber1.83.0 arm64 1.83.0-2.1ubuntu1 [255 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-fiber1.83-dev arm64 1.83.0-2.1ubuntu1 [270 kB] Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-fiber-dev arm64 1.83.0.1ubuntu2 [4486 B] Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-filesystem-dev arm64 1.83.0.1ubuntu2 [4094 B] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph1.83.0 arm64 1.83.0-2.1ubuntu1 [354 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-regex1.83.0 arm64 1.83.0-2.1ubuntu1 [329 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-regex1.83-dev arm64 1.83.0-2.1ubuntu1 [349 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-test1.83.0 arm64 1.83.0-2.1ubuntu1 [444 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-test1.83-dev arm64 1.83.0-2.1ubuntu1 [572 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph1.83-dev arm64 1.83.0-2.1ubuntu1 [397 kB] Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-graph-dev arm64 1.83.0.1ubuntu2 [4160 B] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-9build1 [89.6 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-9build1 [7754 B] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 librdmacm1t64 arm64 50.0-2build1 [70.6 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libfabric1 arm64 1.17.0-3build1 [541 kB] Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc15 arm64 2.10.0-1 [158 kB] Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 libmunge2 arm64 0.5.15-3ubuntu1 [14.8 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libpciaccess0 arm64 0.17-3 [18.6 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu1 [11.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1 [37.3 kB] Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-plugins arm64 2.10.0-1 [15.7 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix2t64 arm64 5.0.1-4.1 [655 kB] Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 libucx0 arm64 1.16.0+ds-4 [1076 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi3t64 arm64 4.1.6-5.1ubuntu1 [2233 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi1.83.0 arm64 1.83.0-2.1ubuntu1 [269 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph-parallel1.83.0 arm64 1.83.0-2.1ubuntu1 [276 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-graph-parallel1.83-dev arm64 1.83.0-2.1ubuntu1 [291 kB] Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-graph-parallel-dev arm64 1.83.0.1ubuntu2 [4192 B] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-2.1ubuntu1 [258 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-iostreams1.83-dev arm64 1.83.0-2.1ubuntu1 [265 kB] Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-iostreams-dev arm64 1.83.0.1ubuntu2 [4046 B] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-json1.83.0 arm64 1.83.0-2.1ubuntu1 [365 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-json1.83-dev arm64 1.83.0-2.1ubuntu1 [387 kB] Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-json-dev arm64 1.83.0.1ubuntu2 [4172 B] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-locale1.83.0 arm64 1.83.0-2.1ubuntu1 [403 kB] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-locale1.83-dev arm64 1.83.0-2.1ubuntu1 [587 kB] Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-locale-dev arm64 1.83.0.1ubuntu2 [4378 B] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-log1.83.0 arm64 1.83.0-2.1ubuntu1 [654 kB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-log1.83-dev arm64 1.83.0-2.1ubuntu1 [946 kB] Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-log-dev arm64 1.83.0.1ubuntu2 [4260 B] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-math1.83.0 arm64 1.83.0-2.1ubuntu1 [431 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-math1.83-dev arm64 1.83.0-2.1ubuntu1 [573 kB] Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-math-dev arm64 1.83.0.1ubuntu2 [4264 B] Get:176 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-common all 4.1.6-5.1ubuntu1 [169 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-3-dev arm64 3.7.0-0.3 [105 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main arm64 libnl-route-3-dev arm64 3.7.0-0.3 [225 kB] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libibverbs-dev arm64 50.0-2build1 [686 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma-dev arm64 2.0.18-1 [39.5 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl7 arm64 2.4.7-7 [40.3 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 libltdl-dev arm64 2.4.7-7 [170 kB] Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 libhwloc-dev arm64 2.10.0-1 [259 kB] Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-2.1-7 arm64 2.1.12-stable-9build1 [140 kB] Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-extra-2.1-7 arm64 2.1.12-stable-9build1 [61.9 kB] Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-openssl-2.1-7 arm64 2.1.12-stable-9build1 [14.7 kB] Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libevent-dev arm64 2.1.12-stable-9build1 [283 kB] Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu1 [894 kB] Get:189 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libpmix-dev arm64 5.0.1-4.1 [4022 kB] Get:190 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:192 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 openmpi-bin arm64 4.1.6-5.1ubuntu1 [113 kB] Get:193 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libopenmpi-dev arm64 4.1.6-5.1ubuntu1 [865 kB] Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-dev arm64 1.15 [3118 B] Get:195 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi1.83-dev arm64 1.83.0-2.1ubuntu1 [299 kB] Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-mpi-dev arm64 1.83.0.1ubuntu2 [4144 B] Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-python1.83.0 arm64 1.83.0-2.1ubuntu1 [307 kB] Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 mpi-default-bin arm64 1.15 [2336 B] Get:199 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi-python1.83.0 arm64 1.83.0-2.1ubuntu1 [353 kB] Get:200 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-mpi-python1.83-dev arm64 1.83.0-2.1ubuntu1 [237 kB] Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-mpi-python-dev arm64 1.83.0.1ubuntu2 [4196 B] Get:202 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-numpy1.83.0 arm64 1.83.0-2.1ubuntu1 [242 kB] Get:203 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-numpy1.83-dev arm64 1.83.0-2.1ubuntu1 [248 kB] Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-numpy-dev arm64 1.83.0.1ubuntu2 [4098 B] Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2.1ubuntu1 [317 kB] Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libboost-program-options1.83-dev arm64 1.83.0-2.1ubuntu1 [390 kB] Get:207 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-program-options-dev arm64 1.83.0.1ubuntu2 [4084 B] Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12t64 arm64 3.12.2-4build2 [2279 kB] Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libexpat1-dev arm64 2.6.1-2 [128 kB] Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3.12-dev arm64 3.12.2-4build2 [5472 kB] Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3-dev arm64 3.12.2-0ubuntu1 [10.1 kB] Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3.12-dev arm64 3.12.2-4build2 [498 kB] Get:213 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libjs-sphinxdoc all 7.2.6-5 [149 kB] Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-dev arm64 3.12.2-0ubuntu1 [26.7 kB] Get:216 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-python1.83-dev arm64 1.83.0-2.1ubuntu1 [336 kB] Get:217 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-python-dev arm64 1.83.0.1ubuntu2 [4346 B] Get:218 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-random1.83.0 arm64 1.83.0-2.1ubuntu1 [242 kB] Get:219 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-random1.83-dev arm64 1.83.0-2.1ubuntu1 [242 kB] Get:220 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-random-dev arm64 1.83.0.1ubuntu2 [4062 B] Get:221 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-regex-dev arm64 1.83.0.1ubuntu2 [4324 B] Get:222 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-serialization-dev arm64 1.83.0.1ubuntu2 [4280 B] Get:223 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-stacktrace1.83.0 arm64 1.83.0-2.1ubuntu1 [288 kB] Get:224 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-stacktrace1.83-dev arm64 1.83.0-2.1ubuntu1 [246 kB] Get:225 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-stacktrace-dev arm64 1.83.0.1ubuntu2 [4066 B] Get:226 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-system-dev arm64 1.83.0.1ubuntu2 [4204 B] Get:227 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-test-dev arm64 1.83.0.1ubuntu2 [4090 B] Get:228 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-thread-dev arm64 1.83.0.1ubuntu2 [4088 B] Get:229 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-timer1.83.0 arm64 1.83.0-2.1ubuntu1 [240 kB] Get:230 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-timer1.83-dev arm64 1.83.0-2.1ubuntu1 [237 kB] Get:231 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-timer-dev arm64 1.83.0.1ubuntu2 [4190 B] Get:232 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-type-erasure1.83.0 arm64 1.83.0-2.1ubuntu1 [244 kB] Get:233 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-type-erasure1.83-dev arm64 1.83.0-2.1ubuntu1 [251 kB] Get:234 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-type-erasure-dev arm64 1.83.0.1ubuntu2 [4162 B] Get:235 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-url1.83.0 arm64 1.83.0-2.1ubuntu1 [342 kB] Get:236 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-url1.83-dev arm64 1.83.0-2.1ubuntu1 [451 kB] Get:237 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-url-dev arm64 1.83.0.1ubuntu2 [4190 B] Get:238 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-wave1.83.0 arm64 1.83.0-2.1ubuntu1 [449 kB] Get:239 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-wave1.83-dev arm64 1.83.0-2.1ubuntu1 [516 kB] Get:240 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-wave-dev arm64 1.83.0.1ubuntu2 [4096 B] Get:241 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-nowide1.83.0 arm64 1.83.0-2.1ubuntu1 [241 kB] Get:242 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libboost-nowide1.83-dev arm64 1.83.0-2.1ubuntu1 [237 kB] Get:243 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-nowide-dev arm64 1.83.0.1ubuntu2 [4136 B] Get:244 http://ftpmaster.internal/ubuntu noble/universe arm64 libboost-all-dev arm64 1.83.0.1ubuntu2 [2286 B] Get:245 http://ftpmaster.internal/ubuntu noble/universe arm64 rapidjson-dev all 1.1.0+dfsg2-7.1 [96.7 kB] Get:246 http://ftpmaster.internal/ubuntu noble/universe arm64 libcereal-dev arm64 1.3.2+dfsg-5 [222 kB] Get:247 http://ftpmaster.internal/ubuntu noble/main arm64 libjson-perl all 4.10000-1 [81.9 kB] Get:248 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] Get:249 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] Get:250 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] Get:251 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] Get:252 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] Get:254 http://ftpmaster.internal/ubuntu noble/universe arm64 libseqan2-dev all 2.4.0+dfsg-16 [1206 kB] Get:255 http://ftpmaster.internal/ubuntu noble/universe arm64 libspoa7.0.0 arm64 4.0.8-1 [53.6 kB] Get:256 http://ftpmaster.internal/ubuntu noble/universe arm64 libspoa-dev arm64 4.0.8-1 [7376 B] Get:257 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-data all 6.1.20170106+dfsg2-1 [4285 kB] Get:258 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] Get:259 http://ftpmaster.internal/ubuntu noble/universe arm64 patchelf arm64 0.18.0-1.1 [98.1 kB] Get:260 http://ftpmaster.internal/ubuntu noble/universe arm64 pybind11-dev all 2.11.1-2 [159 kB] Get:261 http://ftpmaster.internal/ubuntu noble/main arm64 python-babel-localedata all 2.10.3-3build1 [6357 kB] Get:262 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tz all 2024.1-2 [31.4 kB] Get:263 http://ftpmaster.internal/ubuntu noble/main arm64 python3-babel all 2.10.3-3build1 [87.5 kB] Get:264 http://ftpmaster.internal/ubuntu noble/main arm64 python3-certifi all 2023.11.17-1 [165 kB] Get:265 http://ftpmaster.internal/ubuntu noble/main arm64 python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:266 http://ftpmaster.internal/ubuntu noble/main arm64 python3-roman all 3.3-3 [9632 B] Get:267 http://ftpmaster.internal/ubuntu noble/main arm64 python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:268 http://ftpmaster.internal/ubuntu noble/main arm64 python3-idna all 3.6-2 [46.0 kB] Get:269 http://ftpmaster.internal/ubuntu noble/main arm64 python3-imagesize all 1.4.1-1 [6844 B] Get:270 http://ftpmaster.internal/ubuntu noble/main arm64 python3-markupsafe arm64 2.1.5-1 [13.6 kB] Get:271 http://ftpmaster.internal/ubuntu noble/main arm64 python3-jinja2 all 3.1.2-1ubuntu1 [107 kB] Get:272 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] Get:273 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybind11 all 2.11.1-2 [167 kB] Get:274 http://ftpmaster.internal/ubuntu noble/main arm64 python3-urllib3 all 2.0.7-1 [113 kB] Get:275 http://ftpmaster.internal/ubuntu noble/main arm64 python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:276 http://ftpmaster.internal/ubuntu noble/main arm64 python3-snowballstemmer all 2.2.0-4 [59.7 kB] Get:277 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 sphinx-common all 7.2.6-5 [741 kB] Get:278 http://ftpmaster.internal/ubuntu noble/main arm64 python3-alabaster all 0.7.12-1 [17.8 kB] Get:279 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-sphinx all 7.2.6-5 [557 kB] Get:280 http://ftpmaster.internal/ubuntu noble/main arm64 dh-exec arm64 0.29 [25.6 kB] Preconfiguring packages ... Fetched 203 MB in 17s (11.8 MB/s) dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: optipng depends on libpng16-16 (>= 1.6.2-1). (Reading database ... 15797 files and directories currently installed.) Removing libpng16-16:arm64 (1.6.43-1) ... Selecting previously unselected package libpng16-16t64:arm64. (Reading database ... 15787 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-3) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.2-4build2_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.2-4build2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.1-2_arm64.deb ... Unpacking libexpat1:arm64 (2.6.1-2) ... Selecting previously unselected package python3.12-minimal. 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Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... Setting up libbsd0:arm64 (0.12.1-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu1) ... Setting up libldap2:arm64 (2.6.7+dfsg-1~exp1ubuntu6) ... Setting up libboost1.83-tools-dev (1.83.0-2.1ubuntu1) ... Setting up chrpath (0.16-2build1) ... Setting up libblas-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-9build1) ... 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 libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:arm64 (2.1.12-stable-9build1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libboost-wave1.83.0:arm64 (1.83.0-2.1ubuntu1) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libboost-coroutine1.83.0:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-chrono1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libpython3.12-stdlib:arm64 (3.12.2-4build2) ... Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... Setting up libboost-math1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libboost-chrono-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-log1.83.0 (1.83.0-2.1ubuntu1) ... Setting up libboost-math-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3.12 (3.12.2-4build2) ... Setting up libedit2:arm64 (3.1-20230828-1) ... Setting up libboost-system-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libpng-dev:arm64 (1.6.43-3) ... Setting up libboost-serialization1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-locale1.83.0:arm64 (1.83.0-2.1ubuntu1) ... Setting up libcereal-dev (1.3.2+dfsg-5) ... Setting up libevent-openssl-2.1-7:arm64 (2.1.12-stable-9build1) ... Setting up libboost-test1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... Setting up libboost-url1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-tools-dev (1.83.0.1ubuntu2) ... Setting up libboost-filesystem1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-exception-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-nowide-dev (1.83.0.1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up libboost-test-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libpython3.12t64:arm64 (3.12.2-4build2) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-7) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libboost-timer1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libllvm17t64:arm64 (1:17.0.6-8ubuntu1.1) ... Setting up libboost-container1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up gfortran-13 (13.2.0-17ubuntu2) ... Setting up libboost-date-time1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-numpy-dev (1.83.0.1ubuntu2) ... Setting up libevent-dev (2.1.12-stable-9build1) ... Setting up liblapack-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up icu-devtools (74.2-1ubuntu1) ... Setting up libboost-random1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-serialization-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-date-time-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libjs-sphinxdoc (7.2.6-5) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-3build1) ... Setting up xml-core (0.19) ... Setting up libcurl4:arm64 (8.5.0-2ubuntu6) ... Setting up libx11-6:arm64 (2:1.8.7-1) ... Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libboost-url-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libhwloc-dev:arm64 (2.10.0-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build1) ... Setting up libarchive13t64:arm64 (3.7.2-1.1ubuntu1) ... Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... Setting up libboost-timer-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-filesystem-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libpython3-stdlib:arm64 (3.12.2-0ubuntu1) ... Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libboost-thread1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libibverbs1:arm64 (50.0-2build1) ... Setting up libboost-json1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-wave1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libboost-locale1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up ibverbs-providers:arm64 (50.0-2build1) ... Setting up libspoa-dev:arm64 (4.0.8-1) ... Setting up openssh-client (1:9.6p1-3ubuntu7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-type-erasure1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libxext6:arm64 (2:1.3.4-1build1) ... Setting up libboost-random-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-locale-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3 (3.12.2-0ubuntu1) ... Setting up libpython3.12-dev:arm64 (3.12.2-4build2) ... Setting up libboost-wave-dev:arm64 (1.83.0.1ubuntu2) ... Setting up man-db (2.12.0-3build4) ... 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-markupsafe (2.1.5-1) ... Setting up gfortran (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up libboost-container-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-tz (2024.1-2) ... Setting up libboost-type-erasure-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-context1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up libxnvctrl0:arm64 (510.47.03-0ubuntu1) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.3) ... Setting up libboost-coroutine1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1ubuntu1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up libboost-fiber1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up sphinx-common (7.2.6-5) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.2-4build2) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up cmake (3.28.3-1build3) ... Setting up librdmacm1t64:arm64 (50.0-2build1) ... Setting up libboost-coroutine-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-log1.83-dev (1.83.0-2.1ubuntu1) ... Setting up libboost-json-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-regex-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-log-dev (1.83.0.1ubuntu2) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up libboost-thread-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-fiber-dev:arm64 (1.83.0.1ubuntu2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libfabric1:arm64 (1.17.0-3build1) ... Setting up libpython3-dev:arm64 (3.12.2-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up python3-babel (2.10.3-3build1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libboost-iostreams1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up python3-alabaster (0.7.12-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up dh-exec (0.29) ... Setting up libboost-context-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-iostreams-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libibverbs-dev:arm64 (50.0-2build1) ... Setting up libhwloc-plugins:arm64 (2.10.0-1) ... Setting up libboost-graph1.83-dev:arm64 (1.83.0-2.1ubuntu1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.12.2-0ubuntu1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up libboost-python1.83-dev (1.83.0-2.1ubuntu1) ... Setting up libpmix2t64:arm64 (5.0.1-4.1) ... Setting up libhsa-runtime64-1 (5.7.1-1build1) ... Setting up libpmix-dev:arm64 (5.0.1-4.1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20231223ubuntu2) ... Setting up libboost-graph-dev:arm64 (1.83.0.1ubuntu2) ... Setting up libboost-python-dev (1.83.0.1ubuntu2) ... Setting up libamdhip64-5 (5.2.3-12) ... Setting up libucx0:arm64 (1.16.0+ds-4) ... Setting up libopenmpi3t64:arm64 (4.1.6-5.1ubuntu1) ... Setting up libboost-mpi1.83.0 (1.83.0-2.1ubuntu1) ... Setting up openmpi-bin (4.1.6-5.1ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libboost-graph-parallel1.83.0 (1.83.0-2.1ubuntu1) ... Setting up mpi-default-bin (1.15) ... Setting up libopenmpi-dev:arm64 (4.1.6-5.1ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-2.1ubuntu1) ... Setting up libboost-mpi-python1.83.0 (1.83.0-2.1ubuntu1) ... Setting up libboost-graph-parallel-dev (1.83.0.1ubuntu2) ... Setting up mpi-default-dev (1.15) ... Setting up libboost-mpi1.83-dev (1.83.0-2.1ubuntu1) ... Setting up libboost-mpi-dev (1.83.0.1ubuntu2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-2.1ubuntu1) ... Setting up libboost-mpi-python-dev (1.83.0.1ubuntu2) ... Setting up libboost-all-dev (1.83.0.1ubuntu2) ... Processing triggers for libc-bin (2.39-0ubuntu5) ... Processing triggers for systemd (255.4-1ubuntu4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any-amd64 arm64 all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-3ubuntu1 dpkg-dev_1.22.5ubuntu4 g++-13_13.2.0-17ubuntu2 gcc-13_13.2.0-17ubuntu2 libc6-dev_2.39-0ubuntu5 libstdc++-13-dev_13.2.0-17ubuntu2 libstdc++6_14-20240303-1ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.13ubuntu1 apt-utils_2.7.13ubuntu1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu7 base-passwd_3.6.3 bash_5.2.21-2ubuntu2 bash-completion_1:2.11-8 binutils_2.42-3ubuntu1 binutils-aarch64-linux-gnu_2.42-3ubuntu1 binutils-common_2.42-3ubuntu1 bsdextrautils_2.39.3-9ubuntu2 bsdutils_1:2.39.3-9ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5ubuntu1 ca-certificates_20240203 chrpath_0.16-2build1 cmake_3.28.3-1build3 cmake-data_3.28.3-1build3 coreutils_9.4-3ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-17ubuntu2 cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2 cpp-aarch64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu4 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-exec_0.29 dh-python_6.20231223ubuntu2 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.5ubuntu4 dpkg-dev_1.22.5ubuntu4 dwz_0.15-1build5 e2fsprogs_1.47.0-2.3ubuntu1 fakeroot_1.33-1 file_1:5.45-3 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-17ubuntu2 g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2 g++-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-17ubuntu2 gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2 gcc-13-base_13.2.0-17ubuntu2 gcc-14-base_14-20240303-1ubuntu1 gcc-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gfortran_4:13.2.0-7ubuntu1 gfortran-13_13.2.0-17ubuntu2 gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2 gfortran-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gpg_2.4.4-2ubuntu15 gpg-agent_2.4.4-2ubuntu15 gpgconf_2.4.4-2ubuntu15 gpgv_2.4.4-2ubuntu15 grep_3.11-4 groff-base_1.23.0-3build1 gzip_1.12-1ubuntu2 hostname_3.23+nmu2ubuntu1 ibverbs-providers_50.0-2build1 icu-devtools_74.2-1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5.1build2 libacl1_2.3.2-1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build1 libamdhip64-5_5.2.3-12 libapparmor1_4.0.0~beta2-0ubuntu3 libapt-pkg6.0t64_2.7.13ubuntu1 libarchive-zip-perl_1.68-1 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Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shasta_0.11.1-4build2.dsc: no acceptable signature found dpkg-source: info: extracting shasta in /<> dpkg-source: info: unpacking shasta_0.11.1.orig.tar.gz dpkg-source: info: unpacking shasta_0.11.1-4build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying gcc-13-bis.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27851044 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27851044 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27851044 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.11.1-4build2 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3,sphinxdoc dh_clean debian/rules binary-arch dh binary-arch --with python3,sphinxdoc dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DBUILD_ID=0.11.1 \ -DBUILD_STATIC_EXECUTABLE=OFF \ -DBUILD_DYNAMIC_EXECUTABLE=ON cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_ID=0.11.1 -DBUILD_STATIC_EXECUTABLE=OFF -DBUILD_DYNAMIC_EXECUTABLE=ON .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Processor architecture is aarch64 -- CMAKE_SYSTEM_NAME is Linux -- BUILD_STATIC_LIBRARY is ON -- BUILD_STATIC_EXECUTABLE is OFF -- BUILD_DYNAMIC_LIBRARY is ON -- BUILD_DYNAMIC_EXECUTABLE is ON -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.11.1 -- Configuring done (1.4s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<>/obj-aarch64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd obj-aarch64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles /<>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/staticLibrary /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/staticLibrary /<>/obj-aarch64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/dynamicLibrary /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/dynamicLibrary /<>/obj-aarch64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o [ 0%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o [ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY 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-fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /<>/src/AlignmentGraph.cpp [ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -c /<>/src/AssembledSegment.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /<>/src/Assembler.cpp [ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /<>/src/AssemblerAlign.cpp /<>/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /<>/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /<>/src/AssemblerAlign1.cpp [ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /<>/src/AssemblerAlign3.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /<>/src/Alignment.cpp [ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /<>/src/AlignmentGraph.cpp [ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /<>/src/AssemblerAlign4.cpp [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /<>/src/AssembledSegment.cpp [ 7%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /<>/src/AssemblerAlignmentCandidates.cpp [ 7%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -c /<>/src/Assembler.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /<>/src/AssemblerAlignmentGraph.cpp [ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /<>/src/AssemblerAlignments.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /<>/src/AssemblerAnalyzePaths.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /<>/src/AssemblerAssemblyGraph.cpp [ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /<>/src/AssemblerAssemblyGraph2.cpp [ 10%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o -c /<>/src/AssemblerAlign.cpp [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerCompressedAssemblyGraph.cpp /<>/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /<>/src/AssemblerAlign.cpp:1160:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1160 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ In file included from /usr/include/c++/13/bits/exception_ptr.h:41, from /usr/include/c++/13/exception:164, from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/src/iostream.hpp:4, from /<>/src/ReadId.hpp:11, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1023:29: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ 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/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44: In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1013:48: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1043:33: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1033:53: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1203:29: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1193:48: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1224:33: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1214:53: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ [ 11%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /<>/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /<>/src/AssemblerDetangle.cpp [ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /<>/src/AssemblerAlign1.cpp [ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /<>/src/AssemblerHttpServer-Alignments.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /<>/src/AssemblerHttpServer-AssemblyGraph.cpp [ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 14%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o -c /<>/src/AssemblerAlign3.cpp [ 15%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /<>/src/AssemblerHttpServer-MarkerGraph.cpp [ 15%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -c /<>/src/AssemblerHttpServer-Mode3.cpp In file included from /<>/src/AssemblerHttpServer-MarkerGraph.cpp:7: /<>/src/hsv.hpp: In function ‘std::pair shasta::hsvToHsl(double, double)’: /<>/src/hsv.hpp:16:70: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 16 | inline std::pair shasta::hsvToHsl(double SV, double V) | ^ [ 16%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /<>/src/AssemblerHttpServer-ReadGraph.cpp [ 16%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /<>/src/AssemblerAlign4.cpp /<>/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /<>/src/AssemblerHttpServer-ReadGraph.cpp:458:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 458 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AssemblerHttpServer-ReadGraph.cpp:612:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 612 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 17%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -c /<>/src/AssemblerAlignmentCandidates.cpp [ 17%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /<>/src/AssemblerHttpServer-Reads.cpp [ 18%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /<>/src/AssemblerHttpServer.cpp [ 18%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /<>/src/AssemblerInducedAlignments.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerKmers.cpp.o -c /<>/src/AssemblerKmers.cpp [ 19%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o -c /<>/src/AssemblerAlignmentGraph.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /<>/src/AssemblerLowHash.cpp [ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /<>/src/AssemblerMarkerConnectivityGraph.cpp [ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o -c /<>/src/AssemblerAlignments.cpp [ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /<>/src/AssemblerMarkerGraph.cpp [ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /<>/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /<>/src/AssemblerMarkerGraphEdges.cpp [ 22%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o -c /<>/src/AssemblerAnalyzePaths.cpp [ 22%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -c /<>/src/AssemblerMarkers.cpp [ 23%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -c /<>/src/AssemblerAssemblyGraph.cpp [ 23%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /<>/src/AssemblerAssemblyGraph2.cpp [ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o -c /<>/src/AssemblerMode3.cpp In file included from /usr/include/c++/13/bits/exception_ptr.h:41, from /usr/include/c++/13/exception:164, from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /<>/src/iostream.hpp:4, from /<>/src/ReadId.hpp:11, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerAssemblyGraph.cpp:2: In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1023:29: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ 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/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44: In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1013:48: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1043:33: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1033:53: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1203:29: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1193:48: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ In function ‘constexpr std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = unsigned char]’, inlined from ‘constexpr void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from ‘constexpr void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1110:18, inlined from ‘constexpr void std::reverse(_BIter, _BIter) [with _BIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_algo.h:1137:21, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1224:33: /usr/include/c++/13/bits/move.h:199:11: warning: writing 8 bytes into a region of size between 9223372036854775816 and 6 [-Wstringop-overflow=] 199 | __b = _GLIBCXX_MOVE(__tmp); | ^ In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = unsigned char]’, inlined from ‘constexpr _Tp* std::allocator< >::allocate(std::size_t) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/allocator.h:198:40, inlined from ‘static constexpr _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = unsigned char]’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘constexpr void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:395:44, inlined from ‘constexpr std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:332:26, inlined from ‘constexpr std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned char; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:554:47, inlined from ‘void shasta::Assembler::writeGfa1BothStrands(const std::string&)’ at /<>/src/AssemblerAssemblyGraph.cpp:1214:53: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset 9223372036854775802 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ [ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerCompressedAssemblyGraph.cpp [ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -c /<>/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp [ 25%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -c /<>/src/AssemblerOptions.cpp [ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /<>/src/AssemblerDetangle.cpp [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /<>/src/AssemblerReadGraph.cpp In file included from /<>/src/ReadId.hpp:5, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerReadGraph.cpp:3: /<>/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /<>/src/AssemblerReadGraph.cpp:1667:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1667 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /<>/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ /<>/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /<>/src/AssemblerReadGraph.cpp:2053:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2053 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /<>/src/AssemblerReadGraph2.cpp [ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -c /<>/src/AssemblerHttpServer-Alignments.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /<>/src/AssemblerReads.cpp [ 28%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -c /<>/src/AssemblerHttpServer-AssemblyGraph.cpp [ 28%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o -c /<>/src/AssemblyGraph.cpp [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /<>/src/AssemblyGraph2.cpp [ 29%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /<>/src/AssemblyPathGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /<>/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp [ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /<>/src/AssemblerHttpServer-MarkerGraph.cpp [ 31%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /<>/src/AssemblyPathGraph2.cpp [ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -c /<>/src/AssemblerHttpServer-Mode3.cpp In file included from /<>/src/AssemblerHttpServer-MarkerGraph.cpp:7: /<>/src/hsv.hpp: In function ‘std::pair shasta::hsvToHsl(double, double)’: /<>/src/hsv.hpp:16:70: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 16 | inline std::pair shasta::hsvToHsl(double SV, double V) | ^ [ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -c /<>/src/CompactUndirectedGraph.cpp [ 32%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /<>/src/AssemblerHttpServer-ReadGraph.cpp [ 33%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 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-Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /<>/src/AssemblerHttpServer-Reads.cpp [ 34%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -c /<>/src/ConfigurationTable.cpp [ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -c /<>/src/ConsensusCaller.cpp [ 35%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -c /<>/src/Coverage.cpp /<>/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /<>/src/AssemblerHttpServer-ReadGraph.cpp:458:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 458 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AssemblerHttpServer-ReadGraph.cpp:612:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 612 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ [ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -MF 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /<>/src/AssemblerLowHash.cpp [ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /<>/src/AssemblerMarkerConnectivityGraph.cpp [ 40%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result 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-O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o -c /<>/src/MarkerGraph.cpp [ 48%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -c /<>/src/AssemblerReads.cpp In file included from /<>/src/ReadId.hpp:5, from /<>/src/OrientedReadPair.hpp:5, from /<>/src/Alignment.hpp:4, from /<>/src/Assembler.hpp:5, from /<>/src/AssemblerReadGraph.cpp:3: /<>/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: /<>/src/AssemblerReadGraph.cpp:1667:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] 1667 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); | ~~~^~~~~~~~ /<>/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ /<>/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /<>/src/AssemblerReadGraph.cpp:2053:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2053 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o -c /<>/src/MedianConsensusCaller.cpp [ 49%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection 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-Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /<>/src/MemoryMappedVector.cpp [ 51%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o -c /<>/src/ReadGraph.cpp [ 55%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /<>/src/AssemblyPathGraph2.cpp [ 55%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o -c /<>/src/ReadLoader.cpp [ 55%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o -c /<>/src/Reads.cpp [ 56%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o -c /<>/src/Base.cpp [ 56%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && 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&& /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -c /<>/src/CompressedAssemblyGraph.cpp [ 58%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o -c /<>/src/Coverage.cpp [ 61%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o cd 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-std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o -c /<>/src/diploidBayesianPhase.cpp [ 64%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o -c /<>/src/dset64Test.cpp /<>/src/diploidBayesianPhase.cpp: In function ‘std::pair shasta::diploidBayesianPhase(const std::array, 2>&, double)’: /<>/src/diploidBayesianPhase.cpp:27:19: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 27 | double epsilon) | ^ [ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o -c /<>/src/Histogram.cpp [ 65%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o -c /<>/src/extractKmer.cpp [ 65%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o -c /<>/src/filesystem.cpp [ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -c /<>/src/HttpServer.cpp [ 66%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o -c /<>/src/html.cpp [ 67%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o -c /<>/src/mappedCopy.cpp [ 67%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o -c /<>/src/mode3-AssemblyPath.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o -c /<>/src/mode3-Detangler.cpp [ 68%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -c /<>/src/mode3-JaccardGraph.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /<>/src/mode3-LocalAssemblyGraph.cpp [ 69%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /<>/src/mode3-PathGraph.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /<>/src/mode3-JaccardGraph.hpp:29, from /<>/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [ 70%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -c /<>/src/mode3.cpp [ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -c /<>/src/InducedAlignment.cpp [ 71%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /<>/src/LocalAlignmentCandidateGraph.cpp [ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -c /<>/src/performanceLog.cpp [ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion 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-D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /<>/src/runCommandWithTimeout.cpp [ 73%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o -c /<>/src/testSpoa.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /<>/src/testSubsetGraph.cpp [ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -c /<>/src/LocalAlignmentGraph.cpp [ 74%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/<>/dynamicLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /<>/src/LocalAssemblyGraph.cpp [ 76%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /<>/src/LocalMarkerGraph-Write.cpp [ 76%] Linking CXX shared library shasta.so cd /<>/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared 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"CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lpthread -lz -lspoa -llapack -lblas -lpython3.12 -ldl -lm [ 77%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /<>/src/LocalMarkerGraph.cpp make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 77%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/dynamicExecutable /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/dynamicExecutable /<>/obj-aarch64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" 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object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -c /<>/src/LowHash1.cpp [ 78%] Linking CXX executable shastaDynamic cd /<>/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script 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epsilon); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [ 85%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /<>/src/ReferenceOverlapMap.cpp [ 86%] 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-fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o -c /<>/src/mode3-JaccardGraph.cpp [ 94%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /<>/src/mode3-LocalAssemblyGraph.cpp [ 95%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /<>/src/mode3-PathGraph.cpp In file included from /usr/include/c++/13/istream:41, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /usr/include/boost/container_hash/hash.hpp:42, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_set.hpp:20, from /usr/include/boost/unordered_set.hpp:17, from /usr/include/boost/graph/adjacency_list.hpp:20, from /<>/src/mode3-JaccardGraph.hpp:29, from /<>/src/mode3-JaccardGraph.cpp:1: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:51: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In file included from /usr/include/boost/graph/adjacency_list.hpp:255: In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:803:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:806:64: /usr/include/c++/13/ostream:293:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /<>/src/mode3-JaccardGraph.cpp:804:18: /usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here 1966 | delete su; | ^~~~~~~~~ [ 95%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -c /<>/src/mode3.cpp [ 96%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -c /<>/src/performanceLog.cpp [ 96%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /<>/src/platformDependent.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /<>/src/runCommandWithTimeout.cpp [ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /<>/src/shastaLapack.cpp [ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /<>/src/testSpoa.cpp [ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /<>/src/testSubsetGraph.cpp In file included from /<>/src/mode3-LocalAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2436:68, inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2470:72, inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /<>/src/mode3-LocalAssemblyGraph.cpp:146:22: /<>/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t1’ is used uninitialized [-Wuninitialized] 29 | class shasta::mode3::LocalAssemblyGraphVertex { | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: /<>/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); | ^ In copy constructor ‘constexpr shasta::mode3::LocalAssemblyGraphVertex::LocalAssemblyGraphVertex(const shasta::mode3::LocalAssemblyGraphVertex&)’, inlined from ‘boost::detail::adj_list_gen::config::bidir_seq_stored_vertex::bidir_seq_stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2436:68, inlined from ‘boost::detail::adj_list_gen::config::stored_vertex::stored_vertex(const VertexProperty&) [with Graph = boost::adjacency_list; VertexListS = boost::listS; OutEdgeListS = boost::listS; DirectedS = boost::bidirectionalS; VertexProperty = shasta::mode3::LocalAssemblyGraphVertex; EdgeProperty = shasta::mode3::LocalAssemblyGraphEdge; GraphProperty = boost::no_property; EdgeListS = boost::listS]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:2470:72, inlined from ‘typename Config::vertex_descriptor boost::add_vertex(const typename Config::vertex_property_type&, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, listS, bidirectionalS, shasta::mode3::LocalAssemblyGraphVertex, shasta::mode3::LocalAssemblyGraphEdge, no_property, listS>::config>]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:1947:24, inlined from ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’ at /<>/src/mode3-LocalAssemblyGraph.cpp:146:22: /<>/src/mode3-LocalAssemblyGraph.hpp:29:22: warning: ‘.shasta::mode3::LocalAssemblyGraphVertex::t2’ is used uninitialized [-Wuninitialized] 29 | class shasta::mode3::LocalAssemblyGraphVertex { | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/mode3-LocalAssemblyGraph.cpp: In member function ‘void* shasta::mode3::LocalAssemblyGraph::addVertex(uint64_t, uint64_t)’: /<>/src/mode3-LocalAssemblyGraph.cpp:146:67: note: ‘’ declared here 146 | return add_vertex(LocalAssemblyGraphVertex(segmentId, distance), *this); | ^ [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /<>/src/timestamp.cpp [ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/<>/staticLibrary/../src -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/shasta-0.11.1-4build2 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /<>/src/touchMemory.cpp [100%] Linking CXX static library shasta.a cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake cd /<>/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerKmers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyPath.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-Detangler.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-JaccardGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o /usr/bin/ranlib shasta.a make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target shastaStaticLibrary make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v7.2.6 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: [new config] 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [100%] index generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in build/html. make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-aarch64-linux-gnu && make -j4 install DESTDIR=/<>/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/<>/obj-aarch64-linux-gnu/./shasta-install/bin/shasta.a -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/shasta.so -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/shastaDynamic -- 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-- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/RestoreRun.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/ReverseTransitiveReduction.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/RunAssemblies.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SaveRun.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SelectKmers2.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SelectKmers4.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SelectKmersBasedOnFrequency.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SetMarkerGraphEdgeFlags.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SetupRunDirectory.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/SetupSmallRunDirectory.py -- Installing: 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-- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteLocalReadGraphReads.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteMarkers.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteMarkersFrequency.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteOrientedRead.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteOrientedReadPath.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteOrientedReadsBySegment.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteParallelMarkerGraphEdges.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WritePseudoPath.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteRead.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/bin/WriteReadGraphEdges.py -- 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/<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/conf/SimpleBayesianConsensusCaller-8.csv -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Detangle-Before.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/style.css -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Bubble.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/ComputationalMethods.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Python.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/CZI-new-logo.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/BuildingFromSource.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Acknowledgments.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Compatibility.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/CommandLineOptions.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChain.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Detangle-After.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PhasedRegionsNaming.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/gpu-acceleration-results.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/RawAlignment.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Superbubble.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi/Makefile -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi/README -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi/shasta.so -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi/index.rst -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/PythonApi/conf.py -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-3.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/RawAlignmentUnmarked.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/3.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/4.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/7.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/1.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/5.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/6.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/InspectingResults-Images/2.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/ReadGraph2.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Configurations.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Running.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-5.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MakeRelease.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-6.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Commands.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/index.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Prerequisites.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/ReadGraph1.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/BubbleChainPath.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/QuickStart.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-2.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Performance.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Markers.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-8.dot -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/ChooseMemoryOptions.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-4.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/SupportedPlatforms.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/Introduction.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-7.dot.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerAlignment.png -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/ReportingBugs.html -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/doxygen -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/doxygen/README -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/doxygen/Doxyfile -- Installing: /<>/debian/tmp/<>/obj-aarch64-linux-gnu/./shasta-install/docs/MarkerGraph-1.dot make[1]: Leaving directory '/<>/obj-aarch64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a # Rename shastaDynamic to shasta for ease mv debian/shasta/usr/bin/shastaDynamic debian/shasta/usr/bin/shasta # The library is in a more unusual place (nested within /usr/lib), so modify # the ELF chrpath -r /usr/lib/python3/dist-packages \ debian/shasta/usr/bin/shasta debian/shasta/usr/bin/shasta: RUNPATH=/<>/obj-aarch64-linux-gnu/dynamicLibrary: debian/shasta/usr/bin/shasta: new RUNPATH: /usr/lib/python3/dist-packages patchelf \ --replace-needed shasta.so shasta.cpython-312-aarch64-linux-gnu.so \ debian/shasta/usr/bin/shasta make[1]: Leaving directory '/<>' dh_installdocs -a dh_sphinxdoc -a dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_python3 -a I: dh_python3 fs:431: renaming shasta.so to shasta.cpython-312-aarch64-linux-gnu.so debian/rules execute_after_dh_python3-arch make[1]: Entering directory '/<>' patchelf \ --set-soname shasta.cpython-312-aarch64-linux-gnu.so \ /<>/debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-aarch64-linux-gnu.so make[1]: Leaving directory '/<>' dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a debian/rules override_dh_missing make[1]: Entering directory '/<>' # No need to install docker files find debian/tmp -type d -name docker | xargs rm -rf # static library should not be installed find debian/tmp -name shasta.a -delete # dynamic library was installed manually before - so remove it from debian/tmp find debian/tmp -name shasta.so -delete # 11MB of generated docs should go into a separate package if this is considered sensible # FIXME: for the moment do not install these find debian/tmp -name docs | xargs rm -rf # Remove rest of files which have already been installed rm -rf debian/tmp//<> dh_missing --list-missing make[1]: Leaving directory '/<>' dh_dwz -a dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-aarch64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present dh_strip -a f6da8e42f6992660a916a65a7894658e79ff3069 787c681b65572483e8366c04310f9148355ee1ef readelf: Error: no .dynamic section in the dynamic segment objcopy: warning: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-aarch64-linux-gnu.so has a corrupt string table index objcopy: unable to modify 'debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-aarch64-linux-gnu.so' due to errors dh_strip: error: objcopy --only-keep-debug --compress-debug-sections debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-312-aarch64-linux-gnu.so debian/.debhelper/python3-shasta/dbgsym-root/usr/lib/debug/.build-id/78/7c681b65572483e8366c04310f9148355ee1ef.debug returned exit code 1 dh_strip: error: Aborting due to earlier error make: *** [debian/rules:15: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-03-12T11:52:07Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 113136 Build-Time: 1021 Distribution: noble-proposed Fail-Stage: build Host Architecture: arm64 Install-Time: 123 Job: shasta_0.11.1-4build2.dsc Machine Architecture: arm64 Package: shasta Package-Time: 1148 Source-Version: 0.11.1-4build2 Space: 113136 Status: attempted Version: 0.11.1-4build2 -------------------------------------------------------------------------------- Finished at 2024-03-12T11:52:07Z Build needed 00:19:08, 113136k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27851044 Scanning for processes to kill in build PACKAGEBUILD-27851044