Start: 2024-12-03 04:36:47 GMT Package: gubbins Version: 3.4-1 Installed-Size: 482 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-multiprocess, python3-numpy, python3-scipy, python3:any, python3, raxml Recommends: iqtree, fasttree Suggests: r-base-core Description: phylogenetic analysis of genome sequences Homepage: https://sanger-pathogens.github.io/gubbins/ Description-md5: cc258d495d1b902fa507e53b5cc3902e Section: science Priority: optional Filename: pool/main/g/gubbins/gubbins_3.4-1_amd64.deb Size: 95052 MD5sum: 0c46217a8e32d7e718f43fc506cb22bd SHA256: 54644c9fb6f16fcae600f5ec9dd1bcae48a396345dc18f224132023fdfcf7ad3 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt gubbins=3.4-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt gubbins=3.4-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmphq3rw2dp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmphq3rw2dp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmphq3rw2dp/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9349 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6273 kB] Fetched 15.8 MB in 1s (12.7 MB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libcap-ng0 libseccomp2 libsystemd0 libudev1 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 660 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257~rc3-1 [448 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257~rc3-1 [147 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 660 kB in 0s (13.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5150 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-4_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4) over (0.8.5-3+b1) ... Setting up libcap-ng0:amd64 (0.8.5-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5149 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc3-1_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libsystemd0:amd64 (257~rc3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc3-1_amd64.deb ... Unpacking libudev1:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libudev1:amd64 (257~rc3-1) ... Processing triggers for libc-bin (2.40-3) ... 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s DUMP: b5c86d193a7e842cee241697150e980c - 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s INFO: Running scripts post_setup 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'clean'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'clean'] 0m5.0s DEBUG: Recording chroot state 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-divert', '--list'] 0m5.7s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-divert', '--list'] 0m5.7s INFO: Running scripts is_testable 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/is_testable_uninstallable'] 0m5.7s INFO: apt-cache does not know about any of the requested packages 0m5.7s INFO: Running scripts pre_test 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_test_exceptions'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_test_root_password'] 0m5.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_test_root_password'] 0m5.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 0m6.5s DEBUG: No broken symlinks as far as we can find. 0m6.5s INFO: Running scripts pre_install 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_database-server'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_database-server'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_exceptions'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_exceptions'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 0m6.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 0m7.3s DEBUG: No broken symlinks as far as we can find. 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-cache', 'policy'] 0m8.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-cache', 'policy'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-cache', 'policy', 'gubbins'] 0m8.1s DUMP: gubbins: Installed: (none) Candidate: 3.4-1 Version table: 3.4-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-cache', 'policy', 'gubbins'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', '-y', 'install', 'gubbins=3.4-1'] 1m21.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu ibverbs-providers iqtree javascript-common krb5-locales libamd-comgr2 libamdhip64-5 libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libmunge2 libncursesw6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnsl2 libnuma1 libopenjp2-7 libopenmpi3t64 libpciaccess0 libperl5.40 libpixman-1-0 libpmix2t64 libpng16-16t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libraqm0 librdmacm1t64 libreadline8t64 libsframe1 libsharpyuv0 libsqlite3-0 libstdc++-14-dev libtiff6 libtirpc-common libtirpc3t64 libtsan2 libubsan1 libucx0 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libxrender1 libz3-4 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openssl perl perl-modules-5.40 python-biopython-doc python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-dendropy python3-dill python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-multiprocess python3-numpy python3-olefile python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal raxml readline-common rpcsvc-proto sgml-base shared-mime-info w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core Suggested packages: liblocale-gettext-perl cron quota binutils-doc gprofng-gui cpp-doc gcc-14-locales cpp-14-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib g++-14-multilib gcc-14-doc gcc-multilib make autoconf automake libtool flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu r-base-core apache2 | lighttpd | httpd libc-devtools glibc-doc gdbm-l10n low-memory-monitor gpm krb5-doc krb5-user libhwloc-contrib-plugins liblcms2-utils pciutils sensible-utils libstdc++-14-doc man-browser opencl-icd perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 samtools t-coffee wise python3-objgraph gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3.12-venv python3.12-doc binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: python3-biopython The following NEW packages will be installed: adduser binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gubbins ibverbs-providers iqtree javascript-common krb5-locales libamd-comgr2 libamdhip64-5 libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libmunge2 libncursesw6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnsl2 libnuma1 libopenjp2-7 libopenmpi3t64 libpciaccess0 libperl5.40 libpixman-1-0 libpmix2t64 libpng16-16t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libraqm0 librdmacm1t64 libreadline8t64 libsframe1 libsharpyuv0 libsqlite3-0 libstdc++-14-dev libtiff6 libtirpc-common libtirpc3t64 libtsan2 libubsan1 libucx0 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libxrender1 libz3-4 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openssl perl perl-modules-5.40 python-biopython-doc python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-dendropy python3-dill python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-multiprocess python3-numpy python3-olefile python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal raxml readline-common rpcsvc-proto sgml-base shared-mime-info w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core 0 upgraded, 200 newly installed, 0 to remove and 0 not upgraded. Need to get 267 MB of archives. After this operation, 1104 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:11 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 krb5-locales all 1.21.3-3 [101 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 manpages all 6.9.1-1 [1393 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 binutils-common amd64 2.43.1-5 [2631 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libsframe1 amd64 2.43.1-5 [77.1 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libbinutils amd64 2.43.1-5 [529 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libctf-nobfd0 amd64 2.43.1-5 [154 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libctf0 amd64 2.43.1-5 [88.4 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libgprofng0 amd64 2.43.1-5 [797 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 binutils-x86-64-linux-gnu amd64 2.43.1-5 [2257 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 binutils amd64 2.43.1-5 [67.8 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libisl23 amd64 0.27-1 [659 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8 [11.1 MB] Get:47 http://deb.debian.org/debian trixie/main amd64 cpp-14 amd64 14.2.0-8 [1276 B] Get:48 http://deb.debian.org/debian trixie/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Get:49 http://deb.debian.org/debian trixie/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Get:50 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:62 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libcc1-0 amd64 14.2.0-8 [42.8 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:67 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8 [21.4 MB] Get:75 http://deb.debian.org/debian trixie/main amd64 gcc-14 amd64 14.2.0-8 [530 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Get:77 http://deb.debian.org/debian trixie/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Get:78 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.11.10-1 [2461 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-3 [1956 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8 [12.1 MB] Get:85 http://deb.debian.org/debian trixie/main amd64 g++-14 amd64 14.2.0-8 [20.2 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Get:87 http://deb.debian.org/debian trixie/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Get:88 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:134 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4+b1 [1651 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-dill all 0.3.9-1 [83.5 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-multiprocess all 0.70.17-1 [107 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get:144 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1+b1 [1499 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 gubbins amd64 3.4-1 [95.1 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.4-1 [661 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get:169 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:170 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:171 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 iqtree amd64 2.0.7+dfsg-1+b1 [3671 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:183 http://deb.debian.org/debian trixie/main amd64 libglib2.0-data all 2.82.2-3 [1275 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libgpm2 amd64 1.20.7-11+b1 [14.4 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 manpages-dev all 6.9.1-1 [2122 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get:197 http://deb.debian.org/debian trixie/main amd64 python-biopython-doc all 1.84+dfsg-4 [18.2 MB] Get:198 http://deb.debian.org/debian trixie/main amd64 python3-olefile all 0.47-1 [39.3 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 xdg-user-dirs amd64 0.18-1 [54.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 267 MB in 1s (192 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5152 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5472 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libgprofng0:amd64 (2.43.1-5) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up shared-mime-info (2.4-5+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-8) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up cpp-14 (14.2.0-8) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up python-biopython-doc (1.84+dfsg-4) ... Setting up xml-core (0.19) ... Setting up libc6-dev:amd64 (2.40-3) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libgcc-14-dev:amd64 (14.2.0-8) ... Setting up libstdc++-14-dev:amd64 (14.2.0-8) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up binutils-x86-64-linux-gnu (2.43.1-5) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up cpp-x86-64-linux-gnu (4:14.2.0-1) ... Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up binutils (2.43.1-5) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up libpmix2t64:amd64 (5.0.4-1) ... Setting up cpp (4:14.2.0-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-8) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up gcc-x86-64-linux-gnu (4:14.2.0-1) ... Setting up python3.12 (3.12.7-3) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up gcc-14 (14.2.0-8) ... Setting up g++-14-x86-64-linux-gnu (14.2.0-8) ... Setting up libhsa-runtime64-1:amd64 (5.7.1-3) ... Setting up g++-x86-64-linux-gnu (4:14.2.0-1) ... Setting up g++-14 (14.2.0-8) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up gcc (4:14.2.0-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up python3-dill (0.3.9-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up g++ (4:14.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-multiprocess (0.70.17-1) ... Setting up python3-dendropy (4.6.1-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-olefile (0.47-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up iqtree (2.0.7+dfsg-1+b1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-scipy (1.13.1-6) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... Setting up gubbins (3.4-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for libc-bin (2.40-3) ... 1m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', '-y', 'install', 'gubbins=3.4-1'] 1m21.3s INFO: Running scripts post_install 1m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_install_exceptions'] 1m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_install_exceptions'] 1m21.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 1m23.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 1m26.3s DEBUG: No broken symlinks as far as we can find. 1m27.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', '-ac', '--ignore-obsolete'] 1m31.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', '-ac', '--ignore-obsolete'] 1m31.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m31.3s DUMP: 0.15.6 1m31.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m31.3s INFO: Running adequate version 0.15.6 now. 1m31.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'gubbins'] 1m31.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'gubbins'] 1m31.4s INFO: Running scripts pre_remove 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m36.4s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 1m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m36.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_exceptions'] 1m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/pre_remove_exceptions'] 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m36.7s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed binutils binutils 2.43.1-5 install ok installed binutils-common:amd64 binutils-common 2.43.1-5 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.43.1-5 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed cpp cpp 4:14.2.0-1 install ok installed cpp-14 cpp-14 14.2.0-8 install ok installed cpp-14-x86-64-linux-gnu cpp-14-x86-64-linux-gnu 14.2.0-8 install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:14.2.0-1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed fasttree fasttree 2.1.11-2 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed g++ g++ 4:14.2.0-1 install ok installed g++-14 g++-14 14.2.0-8 install ok installed g++-14-x86-64-linux-gnu g++-14-x86-64-linux-gnu 14.2.0-8 install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:14.2.0-1 install ok installed gcc gcc 4:14.2.0-1 install ok installed gcc-14 gcc-14 14.2.0-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu 14.2.0-8 install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:14.2.0-1 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gubbins gubbins 3.4-1 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed ibverbs-providers:amd64 ibverbs-providers 52.0-2+b1 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed iqtree iqtree 2.0.7+dfsg-1+b1 install ok installed javascript-common javascript-common 11+nmu1 install ok installed krb5-locales krb5-locales 1.21.3-3 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2 install ok installed libamdhip64-5 libamdhip64-5 5.7.1-5 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libasan8:amd64 libasan8 14.2.0-8 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libbinutils:amd64 libbinutils 2.43.1-5 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc-dev-bin libc-dev-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libc6-dev:amd64 libc6-dev 2.40-3 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcc1-0:amd64 libcc1-0 14.2.0-8 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.43.1-5 install ok installed libctf0:amd64 libctf0 2.43.1-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.123-1 install ok installed libdrm-common libdrm-common 2.4.123-1 install ok installed libdrm2:amd64 libdrm2 2.4.123-1 install ok installed libedit2:amd64 libedit2 3.1-20240808-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3.1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-8 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libglib2.0-data libglib2.0-data 2.82.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgpm2:amd64 libgpm2 1.20.7-11+b1 install ok installed libgprofng0:amd64 libgprofng0 2.43.1-5 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 5.7.1-3 install ok installed libhsakmt1:amd64 libhsakmt1 5.7.0-1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-8 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.11.2-1 install ok installed libhwloc15:amd64 libhwloc15 2.11.2-1 install ok installed libibmad5:amd64 libibmad5 52.0-2+b1 install ok installed libibumad3:amd64 libibumad3 52.0-2+b1 install ok installed libibverbs1:amd64 libibverbs1 52.0-2+b1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libisl23:amd64 libisl23 0.27-1 install ok installed libitm1:amd64 libitm1 14.2.0-8 install ok installed libjansson4:amd64 libjansson4 2.14-2+b3 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.4.7-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-4 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-18 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblsan0:amd64 liblsan0 14.2.0-8 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b3 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b2 install ok installed libmunge2:amd64 libmunge2 0.5.15-4+b1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.3+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.3+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 install ok installed libopenmpi3t64:amd64 libopenmpi3t64 4.1.6-13.3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.4-1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3 install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-8 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 install ok installed librdmacm1t64:amd64 librdmacm1t64 52.0-2+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsframe1:amd64 libsframe1 2.43.1-5 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtsan2:amd64 libtsan2 14.2.0-8 install ok installed libubsan1:amd64 libubsan1 14.2.0-8 install ok installed libucx0:amd64 libucx0 1.17.0+ds-3 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed linux-libc-dev linux-libc-dev 6.11.10-1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed manpages manpages 6.9.1-1 install ok installed manpages-dev manpages-dev 6.9.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-11 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-5 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1+b2 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed python-biopython-doc python-biopython-doc 1.84+dfsg-4 install ok installed python3 python3 3.12.6-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.84+dfsg-4+b1 install ok installed python3-cairo python3-cairo 1.26.1-2+b1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dendropy python3-dendropy 4.6.1-2 install ok installed python3-dill python3-dill 0.3.9-1 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-multiprocess python3-multiprocess 0.70.17-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-12 install ok installed python3-olefile python3-olefile 0.47-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 74.1.2-2 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.13.1-6 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed raxml raxml 8.2.13+dfsg-1+b1 install ok installed readline-common readline-common 8.2-5 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed shared-mime-info shared-mime-info 2.4-5+b1 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-user-dirs xdg-user-dirs 0.18-1 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 1m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'remove', 'adduser', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++-', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'ibverbs-providers:amd64', 'iqtree', 'javascript-common', 'krb5-locales', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwasan0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmunge2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libstdc++-14-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libucx0:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python-biopython-doc', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-dendropy', 'python3-dill', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-multiprocess', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'shared-mime-info', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'gubbins'] 2m18.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gubbins ibverbs-providers iqtree javascript-common krb5-locales libamd-comgr2 libamdhip64-5 libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libmunge2 libncursesw6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnsl2 libnuma1 libopenjp2-7 libopenmpi3t64 libpciaccess0 libperl5.40 libpixman-1-0 libpmix2t64 libpng16-16t64 libpsm-infinipath1 libpsm2-2 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libraqm0 librdmacm1t64 libreadline8t64 libsframe1 libsharpyuv0 libsqlite3-0 libstdc++-14-dev libtiff6 libtirpc-common libtirpc3t64 libtsan2 libubsan1 libucx0 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libxrender1 libz3-4 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase ocl-icd-libopencl1 openssl perl perl-modules-5.40 python-biopython-doc python3 python3-autocommand python3-biopython python3-cairo python3-chardet python3-decorator python3-dendropy python3-dill python3-freetype python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-multiprocess python3-numpy python3-olefile python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3-scipy python3-typeguard python3-typing-extensions python3.12 python3.12-minimal raxml readline-common rpcsvc-proto sgml-base shared-mime-info w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 200 to remove and 0 not upgraded. After this operation, 1104 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 25946 files and directories currently installed.) Removing iqtree (2.0.7+dfsg-1+b1) ... Removing libopenmpi3t64:amd64 (4.1.6-13.3) ... Removing libucx0:amd64 (1.17.0+ds-3) ... Removing libfabric1:amd64 (1.17.0-3.1) ... Removing librdmacm1t64:amd64 (52.0-2+b1) ... Removing g++ (4:14.2.0-1) ... Removing gcc (4:14.2.0-1) ... Removing g++-x86-64-linux-gnu (4:14.2.0-1) ... Removing gcc-x86-64-linux-gnu (4:14.2.0-1) ... Removing g++-14 (14.2.0-8) ... Removing g++-14-x86-64-linux-gnu (14.2.0-8) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:14.2.0-1) ... Removing cpp-x86-64-linux-gnu (4:14.2.0-1) ... Removing fasttree (2.1.11-2) ... Removing gubbins (3.4-1) ... Removing python3-biopython (1.84+dfsg-4+b1) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2+b1) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-8) ... Removing ibverbs-providers:amd64 (52.0-2+b1) ... Removing javascript-common (11+nmu1) ... Removing krb5-locales (1.21.3-3) ... Removing libamdhip64-5 (5.7.1-5) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Removing libstdc++-14-dev:amd64 (14.2.0-8) ... Removing shared-mime-info (2.4-5+b1) ... Removing python3-pil:amd64 (10.4.0-1+b1) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing python3-scipy (1.13.1-6) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libc6-dev:amd64 (2.40-3) ... Removing libc-dev-bin (2.40-3) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libhsa-runtime64-1:amd64 (5.7.1-3) ... Removing libhsakmt1:amd64 (5.7.0-1) ... Removing libdrm-amdgpu1:amd64 (2.4.123-1) ... Removing libdrm2:amd64 (2.4.123-1) ... Removing libdrm-common (2.4.123-1) ... Removing libllvm17t64:amd64 (1:17.0.6-18) ... Removing libedit2:amd64 (3.1-20240808-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libpmix2t64:amd64 (5.0.4-1) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing ncbi-blast+ (2.16.0+ds-6+b1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-pkg-resources (74.1.2-2) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing libfontenc1:amd64 (1:1.1.8-1+b1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing libglib2.0-data (2.82.2-3) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgpm2:amd64 (1.20.7-11+b1) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libhwloc-plugins:amd64 (2.11.2-1) ... Removing libhwloc15:amd64 (2.11.2-1) ... Removing libibmad5:amd64 (52.0-2+b1) ... Removing libibumad3:amd64 (52.0-2+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing python-biopython-doc (1.84+dfsg-4) ... Removing libjs-sphinxdoc (7.4.7-4) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmbedtls21:amd64 (3.6.2-3) ... Removing libmbedx509-7:amd64 (3.6.2-3) ... Removing libmbedcrypto16:amd64 (3.6.2-3) ... Removing libmunge2:amd64 (0.5.15-4+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpsm2-2 (11.2.185-2.1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libpciaccess0:amd64 (0.17-3+b2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing libxnvctrl0:amd64 (535.171.04-1+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing linux-libc-dev (6.11.10-1) ... Removing manpages-dev (6.9.1-1) ... Removing manpages (6.9.1-1) ... Removing ncbi-data (6.1.20170106+dfsg2-5) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Removing openssl (3.3.2-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-dendropy (4.6.1-2) ... Removing python3-multiprocess (0.70.17-1) ... Removing python3-dill (0.3.9-1) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-olefile (0.47-1) ... Removing raxml (8.2.13+dfsg-1+b1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-user-dirs (0.18-1) ... Removing libibverbs1:amd64 (52.0-2+b1) ... Removing adduser (3.137) ... Removing gcc-14 (14.2.0-8) ... Removing binutils (2.43.1-5) ... Removing gcc-14-x86-64-linux-gnu (14.2.0-8) ... Removing binutils-x86-64-linux-gnu (2.43.1-5) ... Removing libgprofng0:amd64 (2.43.1-5) ... Removing libctf0:amd64 (2.43.1-5) ... Removing libbinutils:amd64 (2.43.1-5) ... Removing binutils-common:amd64 (2.43.1-5) ... Removing cpp-14 (14.2.0-8) ... Removing cpp-14-x86-64-linux-gnu (14.2.0-8) ... Removing libgcc-14-dev:amd64 (14.2.0-8) ... Removing libasan8:amd64 (14.2.0-8) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libcc1-0:amd64 (14.2.0-8) ... Removing libctf-nobfd0:amd64 (2.43.1-5) ... Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libhwasan0:amd64 (14.2.0-8) ... Removing libisl23:amd64 (0.27-1) ... Removing libitm1:amd64 (14.2.0-8) ... Removing libjansson4:amd64 (2.14-2+b3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing liblsan0:amd64 (14.2.0-8) ... Removing libmpc3:amd64 (1.3.1-1+b3) ... Removing libmpfr6:amd64 (4.2.1-1+b2) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.3+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (14.2.0-8) ... Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsframe1:amd64 (2.43.1-5) ... Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libtsan2:amd64 (14.2.0-8) ... Removing libubsan1:amd64 (14.2.0-8) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 2m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'remove', 'adduser', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++-', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'ibverbs-providers:amd64', 'iqtree', 'javascript-common', 'krb5-locales', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwasan0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmunge2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libstdc++-14-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libucx0:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python-biopython-doc', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-dendropy', 'python3-dill', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-multiprocess', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'shared-mime-info', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'gubbins'] 2m18.8s INFO: Running scripts post_remove 2m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_remove_exceptions'] 2m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_remove_exceptions'] 2m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', 'adduser', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'ibverbs-providers:amd64', 'iqtree', 'javascript-common', 'krb5-locales', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwasan0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmunge2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libstdc++-14-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libucx0:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python-biopython-doc', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-dendropy', 'python3-dill', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-multiprocess', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'shared-mime-info', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m19.5s DUMP: (Reading database ... 5255 files and directories currently installed.) Purging configuration files for adduser (3.137) ... dpkg: warning: ignoring request to remove binutils which isn't installed Purging configuration files for binutils-common:amd64 (2.43.1-5) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for cpp (4:14.2.0-1) ... dpkg: warning: ignoring request to remove cpp-14 which isn't installed dpkg: warning: ignoring request to remove cpp-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove cpp-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... dpkg: warning: ignoring request to remove fonts-dejavu-extra which isn't installed Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-14 which isn't installed dpkg: warning: ignoring request to remove g++-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove g++-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-14 which isn't installed dpkg: warning: ignoring request to remove gcc-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc-x86-64-linux-gnu which isn't installed Purging configuration files for ibverbs-providers:amd64 (52.0-2+b1) ... dpkg: warning: ignoring request to remove iqtree which isn't installed Purging configuration files for javascript-common (11+nmu1) ... dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-3) ... dpkg: warning: ignoring request to remove libglib2.0-data which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpm2 which isn't installed dpkg: warning: ignoring request to remove libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibmad5 which isn't installed dpkg: warning: ignoring request to remove libibumad3 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.3+b1) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libopenmpi3t64 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libsframe1 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libstdc++-14-dev which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove manpages which isn't installed dpkg: warning: ignoring request to remove manpages-dev which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-5) ... Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove python-biopython-doc which isn't installed Purging configuration files for python3 (3.12.6-1) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-dill which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-multiprocess which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-olefile which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for shared-mime-info (2.4-5+b1) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23.1) ... Purging configuration files for xdg-user-dirs (0.18-1) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', 'adduser', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fasttree', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'ibverbs-providers:amd64', 'iqtree', 'javascript-common', 'krb5-locales', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwasan0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmunge2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnsl2:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpmix2t64:amd64', 'libpng16-16t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'librdmacm1t64:amd64', 'libreadline8t64:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libstdc++-14-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libucx0:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python-biopython-doc', 'python3', 'python3-autocommand', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-decorator', 'python3-dendropy', 'python3-dill', 'python3-freetype', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-multiprocess', 'python3-numpy', 'python3-olefile', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'raxml', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'shared-mime-info', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', 'gubbins'] 2m19.5s DUMP: dpkg: warning: ignoring request to remove gubbins which isn't installed 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', 'gubbins'] 2m19.5s INFO: Running scripts post_purge 2m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_purge_exceptions'] 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_purge_exceptions'] 2m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', '--pending'] 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--purge', '--pending'] 2m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--remove', '--pending'] 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg', '--remove', '--pending'] 2m19.5s INFO: Running scripts post_test 2m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_test_exceptions'] 2m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'tmp/scripts/post_test_exceptions'] 2m19.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 2m19.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 2m20.2s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 2m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-divert', '--list'] 2m20.3s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'dpkg-divert', '--list'] 2m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'clean'] 2m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp', 'apt-get', 'clean'] 2m20.3s DEBUG: Recording chroot state 2m20.8s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 not owned 2m20.8s INFO: PASS: Installation and purging test. 2m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/shm'] 2m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/shm'] 2m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/console'] 2m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/console'] 2m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/ptmx'] 2m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/ptmx'] 2m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts'] 2m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/dev/pts'] 2m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/proc'] 2m21.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp/proc'] 2m21.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 2m21.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphq3rw2dp'] 2m21.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmphq3rw2dp 2m21.4s INFO: PASS: All tests. 2m21.4s INFO: piuparts run ends. ret=0 End: 2024-12-03 04:39:09 GMT