Start: 2024-03-03 23:07:01 GMT Package: ruby-bio Version: 2.0.5-1 Installed-Size: 2804 Maintainer: Debian Ruby Team Architecture: all Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Breaks: ruby-crb-blast (<< 0.6.9-4) Description: Ruby tools for computational molecular biology Homepage: https://bioruby.org/ Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_2.0.5-1_all.deb Size: 656832 MD5sum: 6b30eeea4b84581b7c9732444564d65b SHA256: 9f50f668237d86011e1cb40b1f1bb964dfb322d827a0a1a7423df712652ac5f3 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --fail-on-broken-symlinks --install-recommends --scriptsdir /etc/piuparts/scripts-broken-symlinks -i :/usr/lib/libcxx/test/std/experimental/filesystem/Inputs/static_test_env/bad_symlink -i :/usr/share/gocode/src/github.com/Masterminds/glide/testdata/path/x/vendor -i :/usr/share/gocode/src/github.com/constabulary/gb/internal/fileutils/_testdata/copyfile/a/rick -i :/usr/share/gocode/src/github.com/hashicorp/atlas-go/archive/test-fixtures/archive-symlink/link/link -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/exe -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/ns/mnt -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/ns/net -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26232/cwd -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26232/root -i :/etc/systemd/system/display-manager.service -i :/usr/share/civicrm/packages/OpenFlashChart/open-flash-chart.swf -I ':/usr/share/mscore3?-.*/sound/sf[2z]' -i :/var/lib/mender -I ':/etc/.*/supervise' -I '/usr/include/python2\.7_d/.*\.h' -I '/usr/include/python3\..dm/.*\.h' -I '/usr/include/python3\..dm/cpython' -I '/usr/include/python3\..dm/internal' -I ':/usr/lib/jvm/java-.*-openjdk-.*/src\.zip' -I ':/usr/share/doc/kde/HTML/.*/common' -I ':/usr/share/man/man1/(.*-)?python.*-config\.1\.gz' -I ':/usr/lib/openjk/Jedi(Academy|Outcast)/base/assets.\.pk3' -I ':/usr/lib/rtcw/main/.*\.(cfg|pk3)' --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt ruby-bio=2.0.5-1 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 1.3.1~202401311836~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --fail-on-broken-symlinks --install-recommends --scriptsdir /etc/piuparts/scripts-broken-symlinks -i :/usr/lib/libcxx/test/std/experimental/filesystem/Inputs/static_test_env/bad_symlink -i :/usr/share/gocode/src/github.com/Masterminds/glide/testdata/path/x/vendor -i :/usr/share/gocode/src/github.com/constabulary/gb/internal/fileutils/_testdata/copyfile/a/rick -i :/usr/share/gocode/src/github.com/hashicorp/atlas-go/archive/test-fixtures/archive-symlink/link/link -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/exe -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/ns/mnt -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26231/ns/net -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26232/cwd -i :/usr/share/gocode/src/github.com/prometheus/procfs/fixtures/26232/root -i :/etc/systemd/system/display-manager.service -i :/usr/share/civicrm/packages/OpenFlashChart/open-flash-chart.swf -I ':/usr/share/mscore3?-.*/sound/sf[2z]' -i :/var/lib/mender -I ':/etc/.*/supervise' -I '/usr/include/python2\.7_d/.*\.h' -I '/usr/include/python3\..dm/.*\.h' -I '/usr/include/python3\..dm/cpython' -I '/usr/include/python3\..dm/internal' -I ':/usr/lib/jvm/java-.*-openjdk-.*/src\.zip' -I ':/usr/share/doc/kde/HTML/.*/common' -I ':/usr/share/man/man1/(.*-)?python.*-config\.1\.gz' -I ':/usr/lib/openjk/Jedi(Academy|Outcast)/base/assets.\.pk3' -I ':/usr/lib/rtcw/main/.*\.(cfg|pk3)' --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt ruby-bio=2.0.5-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpinnze6k3 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpinnze6k3 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/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/tmpinnze6k3/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/tmpinnze6k3/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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/tmpinnze6k3/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-broken-symlinks to /srv/piuparts.debian.org/tmp/tmpinnze6k3/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'update'] 0m4.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9936 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7224 kB] Fetched 17.4 MB in 3s (5677 kB/s) Reading package lists... 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'update'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-yf', 'dist-upgrade'] 0m10.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be REMOVED: libcom-err2 libext2fs2 libgnutls30 libss2 The following NEW packages will be installed: libcom-err2t64 libext2fs2t64 libgnutls30t64 libss2t64 The following packages will be upgraded: apt bsdutils debianutils e2fsprogs libapt-pkg6.0t64 libblkid1 libc-bin libc6 libmount1 libpam-modules libpam-modules-bin libpam-runtime libsmartcols1 libuuid1 logsave mount sysvinit-utils util-linux zlib1g 19 upgraded, 4 newly installed, 4 to remove and 0 not upgraded. Need to get 10.6 MB of archives. After this operation, 10.2 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-9 [97.3 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-9 [1230 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:5 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13+b1 [984 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1 [1425 kB] Get:8 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13+b1 [1368 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:10 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.3 [206 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libss2t64 amd64 1.47.0-2.3 [24.9 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-9 [30.1 kB] Get:14 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.3 [19.9 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libcom-err2t64 amd64 1.47.0-2.3 [20.2 kB] Get:16 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.3 [571 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:19 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-9 [143 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-9 [159 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-9 [191 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-9 [117 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.6 MB in 0s (61.1 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 ... 5234 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-9_amd64.deb ... Unpacking bsdutils (1:2.39.3-9) over (1:2.39.3-6) ... Setting up bsdutils (1:2.39.3-9) ... (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 ... 5234 files and directories currently installed.) Preparing to unpack .../debianutils_5.17_amd64.deb ... Unpacking debianutils (5.17) over (5.16) ... Setting up debianutils (5.17) ... (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 ... 5234 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-9_amd64.deb ... Unpacking util-linux (2.39.3-9) over (2.39.3-6) ... Setting up util-linux (2.39.3-9) ... (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 ... 5234 files and directories currently installed.) Preparing to unpack .../libc6_2.37-15.1_amd64.deb ... Unpacking libc6:amd64 (2.37-15.1) over (2.37-15) ... Setting up libc6:amd64 (2.37-15.1) ... (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 ... 5234 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1) over (1:1.3.dfsg-3+b1) ... Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ... (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 ... 5233 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.13+b1_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.13+b1) over (2.7.13) ... Setting up libapt-pkg6.0t64:amd64 (2.7.13+b1) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.8.1). (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 ... 5234 files and directories currently installed.) Removing libgnutls30:amd64 (3.8.3-1) ... Selecting previously unselected package libgnutls30t64: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 ... 5206 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1) ... (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 ... 5235 files and directories currently installed.) Preparing to unpack .../apt_2.7.13+b1_amd64.deb ... Unpacking apt (2.7.13+b1) over (2.7.13) ... Setting up apt (2.7.13+b1) ... (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 ... 5236 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-15.1_amd64.deb ... Unpacking libc-bin (2.37-15.1) over (2.37-15) ... Setting up libc-bin (2.37-15.1) ... (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 ... 5236 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_amd64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.08-6) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2+b1). (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 ... 5236 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2+b1) ... Selecting previously unselected package libext2fs2t64: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 ... 5228 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.3_amd64.deb ... Unpacking libext2fs2t64:amd64 (1.47.0-2.3) ... dpkg: libss2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libss2 (>= 1.38). (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 ... 5236 files and directories currently installed.) Removing libss2:amd64 (1.47.0-2+b1) ... Selecting previously unselected package libss2t64: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 ... 5230 files and directories currently installed.) Preparing to unpack .../libss2t64_1.47.0-2.3_amd64.deb ... Unpacking libss2t64:amd64 (1.47.0-2.3) ... Preparing to unpack .../libuuid1_2.39.3-9_amd64.deb ... Unpacking libuuid1:amd64 (2.39.3-9) over (2.39.3-6) ... Setting up libuuid1:amd64 (2.39.3-9) ... (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 ... 5236 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.3_amd64.deb ... Unpacking logsave (1.47.0-2.3) over (1.47.0-2+b1) ... dpkg: libcom-err2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libcom-err2 (>= 1.43.9). (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 ... 5235 files and directories currently installed.) Removing libcom-err2:amd64 (1.47.0-2+b1) ... Selecting previously unselected package libcom-err2t64: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 ... 5229 files and directories currently installed.) Preparing to unpack .../libcom-err2t64_1.47.0-2.3_amd64.deb ... Unpacking libcom-err2t64:amd64 (1.47.0-2.3) ... Setting up libcom-err2t64:amd64 (1.47.0-2.3) ... Setting up libext2fs2t64:amd64 (1.47.0-2.3) ... Setting up libss2t64:amd64 (1.47.0-2.3) ... (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 ... 5235 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.3_amd64.deb ... Unpacking e2fsprogs (1.47.0-2.3) over (1.47.0-2+b1) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../libpam-modules-bin_1.5.3-6_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.5.3-4) ... Setting up libpam-modules-bin (1.5.3-6) ... (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 ... 5232 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-6) over (1.5.3-4) ... Setting up libpam-modules:amd64 (1.5.3-6) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../mount_2.39.3-9_amd64.deb ... Unpacking mount (2.39.3-9) over (2.39.3-6) ... Preparing to unpack .../libpam-runtime_1.5.3-6_all.deb ... Unpacking libpam-runtime (1.5.3-6) over (1.5.3-4) ... Setting up libpam-runtime (1.5.3-6) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.3-9_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-9) over (2.39.3-6) ... Setting up libblkid1:amd64 (2.39.3-9) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-9_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-9) over (2.39.3-6) ... Setting up libmount1:amd64 (2.39.3-9) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-9_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-9) over (2.39.3-6) ... Setting up libsmartcols1:amd64 (2.39.3-9) ... Setting up logsave (1.47.0-2.3) ... Setting up mount (2.39.3-9) ... Setting up e2fsprogs (1.47.0-2.3) ... Processing triggers for libc-bin (2.37-15.1) ... 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-yf', 'dist-upgrade'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.4s DUMP: 63994ed7d200009885bd27bb97b4704c - 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m10.4s INFO: Running scripts post_setup 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_dummy_users'] 0m11.5s 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 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_dummy_users'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_fake-essential_unbreak_symlinks'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_fake-essential_unbreak_symlinks'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_forbid_home'] 0m11.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_forbid_home'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_minimize'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_minimize'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_zz_backports'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_setup_zz_backports'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'clean'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'clean'] 0m11.6s DEBUG: Recording chroot state 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.1s DUMP: install ok installed apt apt 2.7.13+b1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-9 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.5 install ok installed e2fsprogs e2fsprogs 1.47.0-2.3 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240221-2.1 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.39.3-9 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.3 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240221-2.1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-9 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0t64:amd64 libpam0t64 1.5.3-4 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-9 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.3 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstdc++6:amd64 libstdc++6 14-20240221-2.1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.3 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-9 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-divert', '--list'] 0m12.1s DUMP: diversion of /lib/x86_64-linux-gnu/libpam.so.0 to /lib/x86_64-linux-gnu/libpam.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpamc.so.0 to /lib/x86_64-linux-gnu/libpamc.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpam.so.0.85.1 to /lib/x86_64-linux-gnu/libpam.so.0.85.1.usr-is-merged by libpam0t64 local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libpam_misc.so.0 to /lib/x86_64-linux-gnu/libpam_misc.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpam_misc.so.0.82.1 to /lib/x86_64-linux-gnu/libpam_misc.so.0.82.1.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpamc.so.0.82.1 to /lib/x86_64-linux-gnu/libpamc.so.0.82.1.usr-is-merged by libpam0t64 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-divert', '--list'] 0m12.1s INFO: Running scripts is_testable 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/is_testable_uninstallable'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/is_testable_uninstallable'] 0m12.1s INFO: apt-cache does not know about any of the requested packages 0m12.1s INFO: Running scripts pre_test 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_test_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_test_exceptions'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_test_root_password'] 0m12.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_test_root_password'] 0m12.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m12.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m12.9s DEBUG: No broken symlinks as far as we can find. 0m12.9s INFO: Running scripts pre_install 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m13.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m13.7s DEBUG: No broken symlinks as far as we can find. 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-cache', 'policy'] 0m14.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-cache', 'policy'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-cache', 'policy', 'ruby-bio'] 0m14.7s DUMP: ruby-bio: Installed: (none) Candidate: 2.0.5-1 Version table: 2.0.5-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-cache', 'policy', 'ruby-bio'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', 'install', 'ruby-bio=2.0.5-1'] 0m37.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libauthen-sasl-perl libbrotli1 libbsd0 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libedit2 libencode-locale-perl libexpat1 libfcgi-perl libfcgi0ldbl libfile-listing-perl libfont-afm-perl libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglib2.0-data libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu72 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmime-tools-perl libmpfr6 libncurses6 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libruby libruby3.1 libsigsegv2 libsoap-lite-perl libsqlite3-0 libssl3t64 libtask-weaken-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.38 perl-openssl-defaults poa prank probcons proda python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip Suggested packages: liblocale-gettext-perl cron quota blends-doc bzip2-doc clustalx seaview wise gawk-doc hmmer-doc apache2 | lighttpd | httpd libdigest-hmac-perl libgssapi-perl gdbm-l10n low-memory-monitor gpm libcrypt-ssleay-perl libapache2-mod-perl2 libmime-lite-perl libnet-jabber-perl libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl libxml-sax-expatxs-perl menu-l10n gksu | kde-cli-tools | ktsuss mustang-testdata perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl debhelper blast2 probcons-extra python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binutils binfmt-support readline-doc ri ruby-dev emboss bundler boxshade t-coffee-examples pymol rasmol Recommended packages: libfcgi-bin blast2 The following packages will be REMOVED: libssl3 The following NEW packages will be installed: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libauthen-sasl-perl libbrotli1 libbsd0 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libedit2 libencode-locale-perl libexpat1 libfcgi-perl libfcgi0ldbl libfile-listing-perl libfont-afm-perl libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglib2.0-data libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu72 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmime-tools-perl libmpfr6 libncurses6 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libruby libruby3.1 libsigsegv2 libsoap-lite-perl libsqlite3-0 libssl3t64 libtask-weaken-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.38 perl-openssl-defaults poa prank probcons proda python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-bio ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip 0 upgraded, 146 newly installed, 1 to remove and 0 not upgraded. Need to get 78.4 MB of archives. After this operation, 354 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:2 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5+b1 [72.8 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5+b1 [48.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:6 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:7 http://deb.debian.org/debian sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3.1 [69.2 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-3.1 [167 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:12 http://deb.debian.org/debian sid/main amd64 gawk amd64 1:5.2.1-2 [673 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3 [817 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3 [1879 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:17 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:18 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3 [1791 kB] Get:22 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3 [597 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:24 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:25 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:26 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:27 http://deb.debian.org/debian sid/main amd64 bzip2 amd64 1.0.8-5+b2 [40.5 kB] Get:28 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:29 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:32 http://deb.debian.org/debian sid/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:33 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:34 http://deb.debian.org/debian sid/main amd64 xz-utils amd64 5.6.0-0.2 [489 kB] Get:35 http://deb.debian.org/debian sid/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get:36 http://deb.debian.org/debian sid/main amd64 menu amd64 2.1.50 [346 kB] Get:37 http://deb.debian.org/debian sid/main amd64 blends-common all 0.7.6 [14.9 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libargtable2-0 amd64 13-1.1 [17.9 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240221-2.1 [136 kB] Get:40 http://deb.debian.org/debian sid/main amd64 clustalo amd64 1.2.4-8 [267 kB] Get:41 http://deb.debian.org/debian sid/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get:42 http://deb.debian.org/debian sid/main amd64 dialign-tx-data all 1.0.2-14 [874 kB] Get:43 http://deb.debian.org/debian sid/main amd64 dialign-tx amd64 1.0.2-14+b1 [86.6 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-1 [1452 kB] Get:45 http://deb.debian.org/debian sid/main amd64 exonerate amd64 2.4.0-5 [1616 kB] Get:46 http://deb.debian.org/debian sid/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:47 http://deb.debian.org/debian sid/main amd64 fsa amd64 1.15.9+dfsg-6 [700 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:50 http://deb.debian.org/debian sid/main amd64 javascript-common all 11+nmu1 [6260 B] Get:51 http://deb.debian.org/debian sid/main amd64 kalign amd64 1:3.3.5-1 [132 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libauthen-sasl-perl all 2.1700-1 [44.8 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.1-1 [129 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libconvert-binhex-perl all 1.125-3 [27.4 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libdata-dump-perl all 1.25-1 [28.4 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libfcgi0ldbl amd64 2.4.2-2 [26.1 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libfcgi-perl amd64 0.82+ds-2+b1 [25.4 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libfont-afm-perl all 1.20-4 [13.1 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240221-2.1 [836 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libglib2.0-data all 2.78.4-3 [1224 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libgpm2 amd64 1.20.7-10+b2 [14.2 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:71 http://deb.debian.org/debian sid/main amd64 liburi-perl all 5.27-1 [98.4 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:74 http://deb.debian.org/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libhtml-format-perl all 2.16-2 [38.8 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libhttp-daemon-perl all 6.16-1 [23.5 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libio-compress-brotli-perl amd64 0.004001-2+b1 [16.9 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libio-sessiondata-perl all 1.03-3 [6316 B] Get:85 http://deb.debian.org/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:86 http://deb.debian.org/debian sid/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libio-stringy-perl all 2.111-3 [56.5 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:90 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libwww-perl all 6.76-1 [183 kB] Get:95 http://deb.debian.org/debian sid/main amd64 liblwp-protocol-https-perl all 6.13-1 [10.7 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libnet-smtp-ssl-perl all 1.04-2 [6548 B] Get:97 http://deb.debian.org/debian sid/main amd64 libmailtools-perl all 2.21-2 [95.6 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libmime-tools-perl all 5.514-1 [203 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:103 http://deb.debian.org/debian sid/main amd64 rubygems-integration all 1.18 [6704 B] Get:104 http://deb.debian.org/debian sid/main amd64 ruby3.1 amd64 3.1.2-8 [663 kB] Get:105 http://deb.debian.org/debian sid/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get:106 http://deb.debian.org/debian sid/main amd64 ruby amd64 1:3.1 [5868 B] Get:107 http://deb.debian.org/debian sid/main amd64 rake all 13.0.6-3 [83.9 kB] Get:108 http://deb.debian.org/debian sid/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:109 http://deb.debian.org/debian sid/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:110 http://deb.debian.org/debian sid/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get:111 http://deb.debian.org/debian sid/main amd64 ruby-sdbm amd64 1.0.0-5+b2 [15.5 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libruby3.1 amd64 3.1.2-8 [5401 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libruby amd64 1:3.1 [4972 B] Get:115 http://deb.debian.org/debian sid/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get:116 http://deb.debian.org/debian sid/main amd64 libxml-parser-perl amd64 2.47-1+b1 [199 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libsoap-lite-perl all 1.27-3 [239 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b2 [313 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libxmlrpc-lite-perl all 0.717-5 [22.4 kB] Get:126 http://deb.debian.org/debian sid/main amd64 lynx-common all 2.9.0rel.0-2 [1193 kB] Get:127 http://deb.debian.org/debian sid/main amd64 lynx amd64 2.9.0rel.0-2 [637 kB] Get:128 http://deb.debian.org/debian sid/main amd64 mafft amd64 7.505-1 [1078 kB] Get:129 http://deb.debian.org/debian sid/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:130 http://deb.debian.org/debian sid/main amd64 med-config all 3.8.1 [11.1 kB] Get:131 http://deb.debian.org/debian sid/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get:132 http://deb.debian.org/debian sid/main amd64 mustang amd64 3.2.4-1 [105 kB] Get:133 http://deb.debian.org/debian sid/main amd64 ncbi-data all 6.1.20170106+dfsg2-1 [3541 kB] Get:134 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.5 MB] Get:135 http://deb.debian.org/debian sid/main amd64 poa amd64 2.0+20060928-8 [53.2 kB] Get:136 http://deb.debian.org/debian sid/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:137 http://deb.debian.org/debian sid/main amd64 probcons amd64 1.12-14 [119 kB] Get:138 http://deb.debian.org/debian sid/main amd64 proda amd64 1.0-14 [65.4 kB] Get:139 http://deb.debian.org/debian sid/main amd64 ruby-bio all 2.0.5-1 [657 kB] Get:140 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-1 [751 kB] Get:141 http://deb.debian.org/debian sid/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] Get:142 http://deb.debian.org/debian sid/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB] Get:143 http://deb.debian.org/debian sid/main amd64 tm-align amd64 20190822+dfsg-2 [865 kB] Get:144 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:145 http://deb.debian.org/debian sid/main amd64 xdg-user-dirs amd64 0.18-1 [54.4 kB] Get:146 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 78.4 MB in 2s (34.6 MB/s) dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: coreutils depends on libssl3 (>= 3.0.0). (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 ... 5232 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... 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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 (8.2-3.1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../9-libsigsegv2_2.14-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1) ... Setting up libmpfr6:amd64 (4.2.1-1+b1) ... Setting up readline-common (8.2-3.1) ... Setting up libreadline8t64:amd64 (8.2-3.1) ... Setting up libsigsegv2:amd64 (2.14-1) ... Selecting previously unselected package gawk. (Reading database ... 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Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../073-libmbedx509-1_2.28.7-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.7-1) ... Selecting previously unselected package libmbedtls14:amd64. Preparing to unpack .../074-libmbedtls14_2.28.7-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.7-1) ... Selecting previously unselected package libmime-tools-perl. Preparing to unpack .../075-libmime-tools-perl_5.514-1_all.deb ... Unpacking libmime-tools-perl (5.514-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../076-libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../077-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../078-ruby3.1_3.1.2-8_amd64.deb ... Unpacking ruby3.1 (3.1.2-8) ... 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Unpacking ruby-sdbm:amd64 (1.0.0-5+b2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../086-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libruby3.1:amd64. Preparing to unpack .../087-libruby3.1_3.1.2-8_amd64.deb ... Unpacking libruby3.1:amd64 (3.1.2-8) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../088-libruby_1%3a3.1_amd64.deb ... Unpacking libruby:amd64 (1:3.1) ... Selecting previously unselected package libtask-weaken-perl. Preparing to unpack .../089-libtask-weaken-perl_1.06-2_all.deb ... Unpacking libtask-weaken-perl (1.06-2) ... Selecting previously unselected package libxml-parser-perl. Preparing to unpack .../090-libxml-parser-perl_2.47-1+b1_amd64.deb ... Unpacking libxml-parser-perl (2.47-1+b1) ... Selecting previously unselected package libsoap-lite-perl. Preparing to unpack .../091-libsoap-lite-perl_1.27-3_all.deb ... Unpacking libsoap-lite-perl (1.27-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../092-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../093-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../094-libxml-sax-base-perl_1.09-3_all.deb ... Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../095-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../096-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b2_amd64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... Selecting previously unselected package libxml-sax-expat-perl. Preparing to unpack .../097-libxml-sax-expat-perl_0.51-2_all.deb ... Unpacking libxml-sax-expat-perl (0.51-2) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../098-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libxmlrpc-lite-perl. Preparing to unpack .../099-libxmlrpc-lite-perl_0.717-5_all.deb ... Unpacking libxmlrpc-lite-perl (0.717-5) ... Selecting previously unselected package lynx-common. Preparing to unpack .../100-lynx-common_2.9.0rel.0-2_all.deb ... Unpacking lynx-common (2.9.0rel.0-2) ... Selecting previously unselected package lynx. Preparing to unpack .../101-lynx_2.9.0rel.0-2_amd64.deb ... Unpacking lynx (2.9.0rel.0-2) ... Selecting previously unselected package mafft. Preparing to unpack .../102-mafft_7.505-1_amd64.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package mailcap. Preparing to unpack .../103-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package med-config. Preparing to unpack .../104-med-config_3.8.1_all.deb ... Unpacking med-config (3.8.1) ... Selecting previously unselected package muscle. Preparing to unpack .../105-muscle_1%3a5.1.0-1_amd64.deb ... Unpacking muscle (1:5.1.0-1) ... Selecting previously unselected package mustang. Preparing to unpack .../106-mustang_3.2.4-1_amd64.deb ... Unpacking mustang (3.2.4-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../107-ncbi-data_6.1.20170106+dfsg2-1_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-1) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../108-ncbi-blast+_2.12.0+ds-4_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-4) ... Selecting previously unselected package poa. Preparing to unpack .../109-poa_2.0+20060928-8_amd64.deb ... Unpacking poa (2.0+20060928-8) ... Selecting previously unselected package prank. Preparing to unpack .../110-prank_0.0.170427+dfsg-3_amd64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package probcons. Preparing to unpack .../111-probcons_1.12-14_amd64.deb ... Unpacking probcons (1.12-14) ... Selecting previously unselected package proda. Preparing to unpack .../112-proda_1.0-14_amd64.deb ... Unpacking proda (1.0-14) ... Selecting previously unselected package ruby-bio. Preparing to unpack .../113-ruby-bio_2.0.5-1_all.deb ... Unpacking ruby-bio (2.0.5-1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../114-shared-mime-info_2.4-1_amd64.deb ... Unpacking shared-mime-info (2.4-1) ... Selecting previously unselected package sim4. Preparing to unpack .../115-sim4_0.0.20121010-8_amd64.deb ... Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package t-coffee. Preparing to unpack .../116-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Selecting previously unselected package tm-align. Preparing to unpack .../117-tm-align_20190822+dfsg-2_amd64.deb ... Unpacking tm-align (20190822+dfsg-2) ... Selecting previously unselected package unzip. Preparing to unpack .../118-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-user-dirs. Preparing to unpack .../119-xdg-user-dirs_0.18-1_amd64.deb ... Unpacking xdg-user-dirs (0.18-1) ... Selecting previously unselected package zip. Preparing to unpack .../120-zip_3.0-13_amd64.deb ... Unpacking zip (3.0-13) ... Setting up media-types (10.1.0) ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up javascript-common (11+nmu1) ... Setting up ncbi-data (6.1.20170106+dfsg2-1) ... Setting up fonts-lato (2.015-1) ... Setting up libgpm2:amd64 (1.20.7-10+b2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up probcons (1.12-14) ... Setting up libfcgi0ldbl:amd64 (2.4.2-2) ... Setting up poa (2.0+20060928-8) ... Setting up xdg-user-dirs (0.18-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up gawk (1:5.2.1-2) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libglib2.0-0:amd64 (2.78.4-1) ... No schema files found: doing nothing. Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.1-1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up file (1:5.45-3) ... Setting up libgomp1:amd64 (14-20240221-2.1) ... Setting up muscle (1:5.1.0-1) ... Setting up bzip2 (1.0.8-5+b2) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up zip (3.0-13) ... Setting up kalign (1:3.3.5-1) ... Setting up libglib2.0-data (2.78.4-3) ... Setting up dialign-tx-data (1.0.2-14) ... Setting up mustang (3.2.4-1) ... Setting up libmbedcrypto7:amd64 (2.28.7-1) ... Setting up proda (1.0-14) ... Setting up sim4 (0.0.20121010-8) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up xz-utils (5.6.0-0.2) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up lynx-common (2.9.0rel.0-2) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libgfortran5:amd64 (14-20240221-2.1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up dialign-tx (1.0.2-14+b1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up netbase (6.4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up menu (2.1.50) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up openssl (3.1.5-1.1) ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up exonerate (2.4.0-5) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0 (13-1.1) ... Setting up libgdbm6:amd64 (1.23-5+b1) ... Setting up ruby-bio (2.0.5-1) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-3) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up clustalo (1.2.4-8) ... Setting up tm-align (20190822+dfsg-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up shared-mime-info (2.4-1) ... Setting up libgdbm-compat4:amd64 (1.23-5+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up lynx (2.9.0rel.0-2) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.8-3) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up python3 (3.11.6-1) ... Setting up rubygems-integration (1.18) ... Setting up perl (5.38.2-3) ... Setting up libdata-dump-perl (1.25-1) ... Setting up libio-compress-brotli-perl (0.004001-2+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libtimedate-perl (2.3300-2) ... Setting up mummer (3.23+dfsg-8) ... Setting up libfcgi-perl (0.82+ds-2+b1) ... Setting up mailcap (3.70+nmu1) ... Setting up liburi-perl (5.27-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1) ... Setting up libio-sessiondata-perl (1.03-3) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libfont-afm-perl (1.20-4) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1+b1) ... Setting up libio-stringy-perl (2.111-3) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libauthen-sasl-perl (2.1700-1) ... Setting up libconvert-binhex-perl (1.125-3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up fsa (1.15.9+dfsg-6) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libhtml-format-perl (2.16-2) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libnet-smtp-ssl-perl (1.04-2) ... Setting up libmailtools-perl (2.21-2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhttp-daemon-perl (6.16-1) ... Setting up libmime-tools-perl (5.514-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libruby:amd64 (1:3.1) ... Setting up libwww-perl (6.76-1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby (1:3.1) ... Setting up rake (13.0.6-3) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b2) ... Setting up liblwp-protocol-https-perl (6.13-1) ... Setting up libxml-parser-perl (2.47-1+b1) ... Setting up libruby3.1:amd64 (3.1.2-8) ... Setting up libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up ruby3.1 (3.1.2-8) ... Setting up libsoap-lite-perl (1.27-3) ... Setting up libxmlrpc-lite-perl (0.717-5) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for menu (2.1.50) ... Setting up blends-common (0.7.6) ... Setting up med-config (3.8.1) ... info: Selecting GID from range 100 to 999 ... info: Adding group `med' (GID 150) ... 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. 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', 'install', 'ruby-bio=2.0.5-1'] 0m37.0s INFO: Running scripts post_install 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_install_exceptions'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_install_exceptions'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_install_extras_unbreak_symlinks'] 0m37.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_install_extras_unbreak_symlinks'] 0m37.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m38.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m39.7s DEBUG: No broken symlinks as far as we can find. 0m39.7s INFO: /bin converted to /usr/bin by /usr merge 0m39.7s INFO: /lib converted to /usr/lib by /usr merge 0m39.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m39.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m39.7s INFO: /sbin converted to /usr/sbin by /usr merge 0m40.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', '-ac', '--ignore-obsolete'] 0m42.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', '-ac', '--ignore-obsolete'] 0m42.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m42.6s DUMP: 0.15.6 0m42.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m42.6s INFO: Running adequate version 0.15.6 now. 0m42.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'ruby-bio'] 0m42.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'ruby-bio'] 0m42.7s INFO: Running scripts pre_remove 0m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_exceptions'] 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/pre_remove_exceptions'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.6s DUMP: install ok installed adduser adduser 3.137 install ok installed amap-align amap-align 2.2+git20080214.600fc29+dfsg-2 install ok installed apt apt 2.7.13+b1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed blends-common blends-common 0.7.6 install ok installed bsdutils bsdutils 1:2.39.3-9 install ok installed bzip2 bzip2 1.0.8-5+b2 install ok installed ca-certificates ca-certificates 20240203 install ok installed clustalo clustalo 1.2.4-8 install ok installed clustalw clustalw 2.1+lgpl-7 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed dialign-tx dialign-tx 1.0.2-14+b1 install ok installed dialign-tx-data dialign-tx-data 1.0.2-14 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.5 install ok installed e2fsprogs e2fsprogs 1.47.0-2.3 install ok installed exonerate exonerate 2.4.0-5 install ok installed file file 1:5.45-3 install ok installed findutils findutils 4.9.0-5 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fsa fsa 1.15.9+dfsg-6 install ok installed gawk gawk 1:5.2.1-2 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240221-2.1 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hmmer hmmer 3.4+dfsg-2 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed javascript-common javascript-common 11+nmu1 install ok installed kalign kalign 1:3.3.5-1 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libargtable2-0 libargtable2-0 13-1.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libauthen-sasl-perl libauthen-sasl-perl 2.1700-1 install ok installed libblkid1:amd64 libblkid1 2.39.3-9 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libclass-inspector-perl libclass-inspector-perl 1.36-3 install ok installed libclone-perl:amd64 libclone-perl 0.46-1+b1 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.3 install ok installed libconvert-binhex-perl libconvert-binhex-perl 1.125-3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdata-dump-perl libdata-dump-perl 1.25-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-6 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.3 install ok installed libfcgi-perl libfcgi-perl 0.82+ds-2+b1 install ok installed libfcgi0ldbl:amd64 libfcgi0ldbl 2.4.2-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfont-afm-perl libfont-afm-perl 1.20-4 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240221-2.1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5+b1 install ok installed libgdbm6:amd64 libgdbm6 1.23-5+b1 install ok installed libgfortran5:amd64 libgfortran5 14-20240221-2.1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-1 install ok installed libglib2.0-data libglib2.0-data 2.78.4-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgomp1:amd64 libgomp1 14-20240221-2.1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgpm2:amd64 libgpm2 1.20.7-10+b2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libhtml-form-perl libhtml-form-perl 6.11-1 install ok installed libhtml-format-perl libhtml-format-perl 2.16-2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.81-1+b1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-6 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-daemon-perl libhttp-daemon-perl 6.16-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 6.45-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-compress-brotli-perl libio-compress-brotli-perl 0.004001-2+b1 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-sessiondata-perl libio-sessiondata-perl 1.03-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.085-1 install ok installed libio-stringy-perl libio-stringy-perl 2.111-3 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.13-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmagic-mgc libmagic-mgc 1:5.45-3 install ok installed libmagic1t64:amd64 libmagic1t64 1:5.45-3 install ok installed libmailtools-perl libmailtools-perl 2.21-2 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmime-tools-perl libmime-tools-perl 5.514-1 install ok installed libmount1:amd64 libmount1 2.39.3-9 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-smtp-ssl-perl libnet-smtp-ssl-perl 1.04-2 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0t64:amd64 libpam0t64 1.5.3-4 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-3.1 install ok installed libruby:amd64 libruby 1:3.1 install ok installed libruby3.1:amd64 libruby3.1 3.1.2-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-9 install ok installed libsoap-lite-perl libsoap-lite-perl 1.27-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.3 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240221-2.1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1 install ok installed libtask-weaken-perl libtask-weaken-perl 1.06-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libudev1:amd64 libudev1 255.4-1 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed liburi-perl liburi-perl 5.27-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-9 install ok installed libwww-perl libwww-perl 6.76-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0207+dfsg+really+2.0134-1+b2 install ok installed libxml-namespacesupport-perl libxml-namespacesupport-perl 1.12-2 install ok installed libxml-parser-perl libxml-parser-perl 2.47-1+b1 install ok installed libxml-sax-base-perl libxml-sax-base-perl 1.09-3 install ok installed libxml-sax-expat-perl libxml-sax-expat-perl 0.51-2 install ok installed libxml-sax-perl libxml-sax-perl 1.02+dfsg-3 install ok installed libxml-simple-perl libxml-simple-perl 2.25-2 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxmlrpc-lite-perl libxmlrpc-lite-perl 0.717-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.3 install ok installed lynx lynx 2.9.0rel.0-2 install ok installed lynx-common lynx-common 2.9.0rel.0-2 install ok installed mafft mafft 7.505-1 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed med-config med-config 3.8.1 install ok installed media-types media-types 10.1.0 install ok installed menu menu 2.1.50 install ok installed mount mount 2.39.3-9 install ok installed mummer mummer 3.23+dfsg-8 install ok installed muscle muscle 1:5.1.0-1 install ok installed mustang mustang 3.2.4-1 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-1 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b1 install ok installed poa poa 2.0+20060928-8 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed probcons probcons 1.12-14 install ok installed proda proda 1.0-14 install ok installed python3 python3 3.11.6-1 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3.11 python3.11 3.11.8-3 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3 install ok installed rake rake 13.0.6-3 install ok installed readline-common readline-common 8.2-3.1 install ok installed ruby ruby 1:3.1 install ok installed ruby-bio ruby-bio 2.0.5-1 install ok installed ruby-net-telnet ruby-net-telnet 0.2.0-1 install ok installed ruby-rubygems ruby-rubygems 3.4.20-1 install ok installed ruby-sdbm:amd64 ruby-sdbm 1.0.0-5+b2 install ok installed ruby-webrick ruby-webrick 1.8.1-1 install ok installed ruby-xmlrpc ruby-xmlrpc 0.3.2-2 install ok installed ruby3.1 ruby3.1 3.1.2-8 install ok installed rubygems-integration rubygems-integration 1.18 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed shared-mime-info shared-mime-info 2.4-1 install ok installed sim4 sim4 0.0.20121010-8 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed t-coffee t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tm-align tm-align 20190822+dfsg-2 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-9 install ok installed xdg-user-dirs xdg-user-dirs 0.18-1 install ok installed xz-utils xz-utils 5.6.0-0.2 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libssl3:amd64=3.1.5-1', 'adduser-', 'amap-align-', 'blends-common-', 'bzip2-', 'ca-certificates-', 'clustalo-', 'clustalw-', 'dialign-tx-', 'dialign-tx-data-', 'exonerate-', 'file-', 'fonts-lato-', 'fsa-', 'gawk-', 'hmmer-', 'javascript-common-', 'kalign-', 'libargtable2-0-', 'libauthen-sasl-perl-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libclass-inspector-perl-', 'libclone-perl:amd64-', 'libconvert-binhex-perl-', 'libdata-dump-perl-', 'libdivsufsort3:amd64-', 'libedit2:amd64-', 'libencode-locale-perl-', 'libexpat1:amd64-', 'libfcgi-perl-', 'libfcgi0ldbl:amd64-', 'libfile-listing-perl-', 'libfont-afm-perl-', 'libgdbm-compat4:amd64-', 'libgdbm6:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-data-', 'libgomp1:amd64-', 'libgpm2:amd64-', 'libhtml-form-perl-', 'libhtml-format-perl-', 'libhtml-parser-perl:amd64-', 'libhtml-tagset-perl-', 'libhtml-tree-perl-', 'libhttp-cookies-perl-', 'libhttp-daemon-perl-', 'libhttp-date-perl-', 'libhttp-message-perl-', 'libhttp-negotiate-perl-', 'libicu72:amd64-', 'libio-compress-brotli-perl-', 'libio-html-perl-', 'libio-sessiondata-perl-', 'libio-socket-ssl-perl-', 'libio-stringy-perl-', 'libjs-jquery-', 'liblmdb0:amd64-', 'liblwp-mediatypes-perl-', 'liblwp-protocol-https-perl-', 'libmagic-mgc-', 'libmagic1t64:amd64-', 'libmailtools-perl-', 'libmbedcrypto7:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-1:amd64-', 'libmime-tools-perl-', 'libmpfr6:amd64-', 'libncurses6:amd64-', 'libncursesw6:amd64-', 'libnet-http-perl-', 'libnet-smtp-ssl-perl-', 'libnet-ssleay-perl:amd64-', 'libperl5.38:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libreadline8t64:amd64-', 'libruby:amd64-', 'libruby3.1:amd64-', 'libsigsegv2:amd64-', 'libsoap-lite-perl-', 'libsqlite3-0:amd64-', 'libssl3t64:amd64-', 'libtask-weaken-perl-', 'libtimedate-perl-', 'libtry-tiny-perl-', 'liburi-perl-', 'libwww-perl-', 'libwww-robotrules-perl-', 'libxml-libxml-perl-', 'libxml-namespacesupport-perl-', 'libxml-parser-perl-', 'libxml-sax-base-perl-', 'libxml-sax-expat-perl-', 'libxml-sax-perl-', 'libxml-simple-perl-', 'libxml2:amd64-', 'libxmlrpc-lite-perl-', 'libyaml-0-2:amd64-', 'lynx-', 'lynx-common-', 'mafft-', 'mailcap-', 'med-config-', 'media-types-', 'menu-', 'mummer-', 'muscle-', 'mustang-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'perl-', 'perl-modules-5.38-', 'perl-openssl-defaults:amd64-', 'poa-', 'prank-', 'probcons-', 'proda-', 'python3-', 'python3-minimal-', 'python3.11-', 'python3.11-minimal-', 'rake-', 'readline-common-', 'ruby-', 'ruby-net-telnet-', 'ruby-rubygems-', 'ruby-sdbm:amd64-', 'ruby-webrick-', 'ruby-xmlrpc-', 'ruby3.1-', 'rubygems-integration-', 'sensible-utils-', 'shared-mime-info-', 'sim4-', 't-coffee-', 'tm-align-', 'ucf-', 'unzip-', 'xdg-user-dirs-', 'xz-utils-', 'zip-', 'ruby-bio-'] 0m50.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libauthen-sasl-perl libbrotli1 libbsd0 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libedit2 libencode-locale-perl libexpat1 libfcgi-perl libfcgi0ldbl libfile-listing-perl libfont-afm-perl libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libglib2.0-data libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libicu72 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto7 libmbedtls14 libmbedx509-1 libmime-tools-perl libmpfr6 libncurses6 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libruby libruby3.1 libsigsegv2 libsoap-lite-perl libsqlite3-0 libssl3t64 libtask-weaken-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.38 perl-openssl-defaults poa prank probcons proda python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-bio ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip The following NEW packages will be installed: libssl3 0 upgraded, 1 newly installed, 146 to remove and 0 not upgraded. Need to get 2063 kB of archives. After this operation, 354 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2063 kB in 0s (22.7 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 ... 15467 files and directories currently installed.) Removing med-config (3.8.1) ... Removing blends-common (0.7.6) ... Removing adduser (3.137) ... Removing amap-align (2.2+git20080214.600fc29+dfsg-2) ... Removing bzip2 (1.0.8-5+b2) ... Removing libxml-simple-perl (2.25-2) ... Removing libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing clustalo (1.2.4-8) ... Removing clustalw (2.1+lgpl-7) ... Removing dialign-tx (1.0.2-14+b1) ... Removing dialign-tx-data (1.0.2-14) ... Removing fsa (1.15.9+dfsg-6) ... Removing exonerate (2.4.0-5) ... Removing file (1:5.45-3) ... Removing fonts-lato (2.015-1) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing hmmer (3.4+dfsg-2) ... Removing javascript-common (11+nmu1) ... Removing kalign (1:3.3.5-1) ... Removing libargtable2-0 (13-1.1) ... Removing libauthen-sasl-perl (2.1700-1) ... Removing lynx (2.9.0rel.0-2) ... Removing libio-compress-brotli-perl (0.004001-2+b1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxmlrpc-lite-perl (0.717-5) ... Removing libsoap-lite-perl (1.27-3) ... Removing libclass-inspector-perl (1.36-3) ... Removing libmime-tools-perl (5.514-1) ... Removing libconvert-binhex-perl (1.125-3) ... Removing libdata-dump-perl (1.25-1) ... Removing libdivsufsort3:amd64 (2.0.1-6) ... Removing ncbi-blast+ (2.12.0+ds-4) ... Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.8-3) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.8-3) ... Removing libfcgi-perl (0.82+ds-2+b1) ... Removing libfcgi0ldbl:amd64 (2.4.2-2) ... Removing libhtml-format-perl (2.16-2) ... Removing libfont-afm-perl (1.20-4) ... Removing mailcap (3.70+nmu1) ... Removing mafft (7.505-1) ... Removing libhttp-daemon-perl (6.16-1) ... Removing libmailtools-perl (2.21-2) ... Removing libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::PurePerl with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Removing tm-align (20190822+dfsg-2) ... Removing libgfortran5:amd64 (14-20240221-2.1) ... Removing shared-mime-info (2.4-1) ... Removing libglib2.0-0:amd64 (2.78.4-1) ... Removing libglib2.0-data (2.78.4-3) ... Removing muscle (1:5.1.0-1) ... Removing libgomp1:amd64 (14-20240221-2.1) ... Removing libgpm2:amd64 (1.20.7-10+b2) ... Removing libhtml-form-perl (6.11-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libio-sessiondata-perl (1.03-3) ... Removing libnet-smtp-ssl-perl (1.04-2) ... Removing libio-stringy-perl (2.111-3) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... Removing libmagic1t64:amd64 (1:5.45-3) ... Removing libmagic-mgc (1:5.45-3) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3.11-minimal:amd64 (3.11.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-3.1) ... 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 libsigsegv2:amd64 (2.14-1) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing libxml-parser-perl (2.47-1+b1) ... Removing libexpat1:amd64 (2.6.0-1) ... Removing liblwp-protocol-https-perl (6.13-1) ... Removing libio-socket-ssl-perl (2.085-1) ... Removing libnet-ssleay-perl:amd64 (1.94-1) ... Removing perl-openssl-defaults:amd64 (7+b1) ... Removing libruby3.1:amd64 (3.1.2-8) ... Removing rake (13.0.6-3) ... Removing ruby (1:3.1) ... Removing ruby-rubygems (3.4.20-1) ... Removing libwww-perl (6.76-1) ... Removing ruby-sdbm:amd64 (1.0.0-5+b2) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libbsd0:amd64 (0.12.1-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.16-1) ... Removing libhttp-cookies-perl (6.11-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.81-1+b1) ... Removing libhtml-tagset-perl (3.20-6) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libnet-http-perl (6.23-1) ... Removing libruby:amd64 (1:3.1) ... Removing ruby3.1 (3.1.2-8) ... Removing rubygems-integration (1.18) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.45-1) ... Removing libclone-perl:amd64 (0.46-1+b1) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.06-1) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing openssl (3.1.5-1.1) ... dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libgdbm6 (>= 1.21). libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16). Removing libgdbm6:amd64 (1.23-5+b1) ... dpkg: perl: dependency problems, but removing anyway as you requested: libxml-sax-base-perl depends on perl:any. libxml-namespacesupport-perl depends on perl:any. libwww-robotrules-perl depends on perl. liburi-perl depends on perl:any. libtry-tiny-perl depends on perl:any. libtimedate-perl depends on perl:any. libtask-weaken-perl depends on perl:any. Removing perl (5.38.2-3) ... Removing libperl5.38:amd64 (5.38.2-3) ... Removing libgdbm-compat4:amd64 (1.23-5+b1) ... Selecting previously unselected package libssl3: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 ... 8121 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) ... Replaced by files in installed package libssl3t64:amd64 (3.1.5-1.1) ... dpkg: libssl3t64:amd64: dependency problems, but removing anyway as you requested: coreutils depends on libssl3 (>= 3.0.0); however: Package libssl3:amd64 is not configured yet. Package libssl3t64:amd64 which provides libssl3 is to be removed. (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 ... 8125 files and directories currently installed.) Removing libssl3t64:amd64 (3.1.5-1.1) ... Setting up libssl3:amd64 (3.1.5-1) ... (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 ... 8113 files and directories currently installed.) Removing libtask-weaken-perl (1.06-2) ... Removing libtimedate-perl (2.3300-2) ... Removing libtry-tiny-perl (0.31-2) ... Removing libwww-robotrules-perl (6.02-1) ... Removing liburi-perl (5.27-1) ... Removing libxml-namespacesupport-perl (1.12-2) ... Removing libxml-sax-base-perl (1.09-3) ... Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing lynx-common (2.9.0rel.0-2) ... Removing media-types (10.1.0) ... Removing menu (2.1.50) ... Removing mustang (3.2.4-1) ... Removing ncbi-data (6.1.20170106+dfsg2-1) ... Removing netbase (6.4) ... Removing perl-modules-5.38 (5.38.2-3) ... Removing poa (2.0+20060928-8) ... Removing prank (0.0.170427+dfsg-3) ... Removing probcons (1.12-14) ... Removing proda (1.0-14) ... Removing readline-common (8.2-3.1) ... Removing ruby-bio (2.0.5-1) ... Removing ruby-net-telnet (0.2.0-1) ... Removing ruby-xmlrpc (0.3.2-2) ... Removing ruby-webrick (1.8.1-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing sim4 (0.0.20121010-8) ... Removing t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Removing unzip (6.0-28) ... Removing xdg-user-dirs (0.18-1) ... Removing xz-utils (5.6.0-0.2) ... Removing zip (3.0-13) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libssl3:amd64=3.1.5-1', 'adduser-', 'amap-align-', 'blends-common-', 'bzip2-', 'ca-certificates-', 'clustalo-', 'clustalw-', 'dialign-tx-', 'dialign-tx-data-', 'exonerate-', 'file-', 'fonts-lato-', 'fsa-', 'gawk-', 'hmmer-', 'javascript-common-', 'kalign-', 'libargtable2-0-', 'libauthen-sasl-perl-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libclass-inspector-perl-', 'libclone-perl:amd64-', 'libconvert-binhex-perl-', 'libdata-dump-perl-', 'libdivsufsort3:amd64-', 'libedit2:amd64-', 'libencode-locale-perl-', 'libexpat1:amd64-', 'libfcgi-perl-', 'libfcgi0ldbl:amd64-', 'libfile-listing-perl-', 'libfont-afm-perl-', 'libgdbm-compat4:amd64-', 'libgdbm6:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-data-', 'libgomp1:amd64-', 'libgpm2:amd64-', 'libhtml-form-perl-', 'libhtml-format-perl-', 'libhtml-parser-perl:amd64-', 'libhtml-tagset-perl-', 'libhtml-tree-perl-', 'libhttp-cookies-perl-', 'libhttp-daemon-perl-', 'libhttp-date-perl-', 'libhttp-message-perl-', 'libhttp-negotiate-perl-', 'libicu72:amd64-', 'libio-compress-brotli-perl-', 'libio-html-perl-', 'libio-sessiondata-perl-', 'libio-socket-ssl-perl-', 'libio-stringy-perl-', 'libjs-jquery-', 'liblmdb0:amd64-', 'liblwp-mediatypes-perl-', 'liblwp-protocol-https-perl-', 'libmagic-mgc-', 'libmagic1t64:amd64-', 'libmailtools-perl-', 'libmbedcrypto7:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-1:amd64-', 'libmime-tools-perl-', 'libmpfr6:amd64-', 'libncurses6:amd64-', 'libncursesw6:amd64-', 'libnet-http-perl-', 'libnet-smtp-ssl-perl-', 'libnet-ssleay-perl:amd64-', 'libperl5.38:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libreadline8t64:amd64-', 'libruby:amd64-', 'libruby3.1:amd64-', 'libsigsegv2:amd64-', 'libsoap-lite-perl-', 'libsqlite3-0:amd64-', 'libssl3t64:amd64-', 'libtask-weaken-perl-', 'libtimedate-perl-', 'libtry-tiny-perl-', 'liburi-perl-', 'libwww-perl-', 'libwww-robotrules-perl-', 'libxml-libxml-perl-', 'libxml-namespacesupport-perl-', 'libxml-parser-perl-', 'libxml-sax-base-perl-', 'libxml-sax-expat-perl-', 'libxml-sax-perl-', 'libxml-simple-perl-', 'libxml2:amd64-', 'libxmlrpc-lite-perl-', 'libyaml-0-2:amd64-', 'lynx-', 'lynx-common-', 'mafft-', 'mailcap-', 'med-config-', 'media-types-', 'menu-', 'mummer-', 'muscle-', 'mustang-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'perl-', 'perl-modules-5.38-', 'perl-openssl-defaults:amd64-', 'poa-', 'prank-', 'probcons-', 'proda-', 'python3-', 'python3-minimal-', 'python3.11-', 'python3.11-minimal-', 'rake-', 'readline-common-', 'ruby-', 'ruby-net-telnet-', 'ruby-rubygems-', 'ruby-sdbm:amd64-', 'ruby-webrick-', 'ruby-xmlrpc-', 'ruby3.1-', 'rubygems-integration-', 'sensible-utils-', 'shared-mime-info-', 'sim4-', 't-coffee-', 'tm-align-', 'ucf-', 'unzip-', 'xdg-user-dirs-', 'xz-utils-', 'zip-', 'ruby-bio-'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libssl3:amd64=3.1.5-1'] 0m51.6s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/2063 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 5279 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) over (3.1.5-1) ... Setting up libssl3:amd64 (3.1.5-1) ... Processing triggers for libc-bin (2.37-15.1) ... 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libssl3:amd64=3.1.5-1'] 0m51.6s INFO: Running scripts post_remove 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_remove_exceptions'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_remove_exceptions'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libedit2:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-perl', 'libfcgi0ldbl:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libicu72:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libsqlite3-0:amd64', 'libssl3t64:amd64', 'libtask-weaken-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'proda', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-net-telnet', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip'] 0m52.2s DUMP: (Reading database ... 5285 files and directories currently installed.) Purging configuration files for adduser (3.137) ... dpkg: warning: ignoring request to remove amap-align which isn't installed Purging configuration files for blends-common (0.7.6) ... dpkg: warning: ignoring request to remove bzip2 which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove clustalo which isn't installed Purging configuration files for clustalw (2.1+lgpl-7) ... dpkg: warning: ignoring request to remove dialign-tx which isn't installed dpkg: warning: ignoring request to remove dialign-tx-data which isn't installed dpkg: warning: ignoring request to remove exonerate which isn't installed dpkg: warning: ignoring request to remove file which isn't installed dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fsa which isn't installed Purging configuration files for gawk (1:5.2.1-2) ... dpkg: warning: ignoring request to remove hmmer which isn't installed Purging configuration files for javascript-common (11+nmu1) ... dpkg: warning: ignoring request to remove kalign which isn't installed dpkg: warning: ignoring request to remove libargtable2-0 which isn't installed dpkg: warning: ignoring request to remove libauthen-sasl-perl which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libclass-inspector-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconvert-binhex-perl which isn't installed dpkg: warning: ignoring request to remove libdata-dump-perl which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfcgi-perl which isn't installed dpkg: warning: ignoring request to remove libfcgi0ldbl which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfont-afm-perl which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.4-1) ... 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 libhtml-form-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-format-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-daemon-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-compress-brotli-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-sessiondata-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-stringy-perl which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1t64:amd64 (1:5.45-3) ... dpkg: warning: ignoring request to remove libmailtools-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmime-tools-perl which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-smtp-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.38 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-3.1) ... dpkg: warning: ignoring request to remove libruby which isn't installed dpkg: warning: ignoring request to remove libruby3.1 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsoap-lite-perl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3t64 which isn't installed dpkg: warning: ignoring request to remove libtask-weaken-perl which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libxml-libxml-perl which isn't installed dpkg: warning: ignoring request to remove libxml-namespacesupport-perl which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-base-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-expat-perl which isn't installed Purging configuration files for libxml-sax-perl (1.02+dfsg-3) ... dpkg: warning: ignoring request to remove libxml-simple-perl which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmlrpc-lite-perl which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for lynx (2.9.0rel.0-2) ... Purging configuration files for lynx-common (2.9.0rel.0-2) ... dpkg: warning: ignoring request to remove mafft which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for med-config (3.8.1) ... Purging configuration files for media-types (10.1.0) ... Purging configuration files for menu (2.1.50) ... dpkg: warning: ignoring request to remove mummer which isn't installed dpkg: warning: ignoring request to remove muscle which isn't installed dpkg: warning: ignoring request to remove mustang which isn't installed dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-1) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for perl (5.38.2-3) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove poa which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed dpkg: warning: ignoring request to remove probcons which isn't installed dpkg: warning: ignoring request to remove proda which isn't installed Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-3) ... dpkg: warning: ignoring request to remove rake which isn't installed Purging configuration files for readline-common (8.2-3.1) ... dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby-rubygems which isn't installed dpkg: warning: ignoring request to remove ruby-sdbm which isn't installed dpkg: warning: ignoring request to remove ruby-webrick which isn't installed dpkg: warning: ignoring request to remove ruby-xmlrpc which isn't installed dpkg: warning: ignoring request to remove ruby3.1 which isn't installed dpkg: warning: ignoring request to remove rubygems-integration which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for shared-mime-info (2.4-1) ... dpkg: warning: ignoring request to remove sim4 which isn't installed dpkg: warning: ignoring request to remove t-coffee which isn't installed dpkg: warning: ignoring request to remove tm-align which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for xdg-user-dirs (0.18-1) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libbsd0:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libedit2:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-perl', 'libfcgi0ldbl:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libicu72:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libsqlite3-0:amd64', 'libssl3t64:amd64', 'libtask-weaken-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'liburi-perl', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'proda', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-net-telnet', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip'] 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', 'ruby-bio'] 0m52.2s DUMP: dpkg: warning: ignoring request to remove ruby-bio which isn't installed 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', 'ruby-bio'] 0m52.2s INFO: Running scripts post_purge 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_purge_exceptions'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_purge_exceptions'] 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', '--pending'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--purge', '--pending'] 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--remove', '--pending'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg', '--remove', '--pending'] 0m52.2s INFO: Running scripts post_test 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_test_exceptions'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'tmp/scripts/post_test_exceptions'] 0m52.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m52.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m53.0s DEBUG: No broken symlinks as far as we can find. 0m53.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-divert', '--list'] 0m53.0s DUMP: diversion of /lib/x86_64-linux-gnu/libpam.so.0 to /lib/x86_64-linux-gnu/libpam.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpamc.so.0 to /lib/x86_64-linux-gnu/libpamc.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpam.so.0.85.1 to /lib/x86_64-linux-gnu/libpam.so.0.85.1.usr-is-merged by libpam0t64 local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libpam_misc.so.0 to /lib/x86_64-linux-gnu/libpam_misc.so.0.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpam_misc.so.0.82.1 to /lib/x86_64-linux-gnu/libpam_misc.so.0.82.1.usr-is-merged by libpam0t64 diversion of /lib/x86_64-linux-gnu/libpamc.so.0.82.1 to /lib/x86_64-linux-gnu/libpamc.so.0.82.1.usr-is-merged by libpam0t64 0m53.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'dpkg-divert', '--list'] 0m53.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'clean'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpinnze6k3', 'apt-get', 'clean'] 0m53.1s DEBUG: Recording chroot state 0m53.6s INFO: PASS: Installation and purging test. 0m53.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/shm'] 0m53.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/shm'] 0m53.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/console'] 0m53.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/console'] 0m53.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/ptmx'] 0m53.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/ptmx'] 0m53.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/pts'] 0m53.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/dev/pts'] 0m53.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/proc'] 0m53.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpinnze6k3/proc'] 0m53.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m54.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpinnze6k3'] 0m54.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpinnze6k3 0m54.1s INFO: PASS: All tests. 0m54.1s INFO: piuparts run ends. ret=0 End: 2024-03-03 23:07:55 GMT