Start: 2025-04-16 03:30:48 GMT [testing] Package: ariba Version: 2.14.7+ds-7 Installed-Size: 20596 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.14), python3 (>= 3.12~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-pkg-resources, python3-tk Suggests: spades Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-7_amd64.deb Size: 1957620 MD5sum: 35d5f2dd2bc36825173336d5988a649d SHA256: 8f5128a7633fcc13c4677f4ab6de6d8311df028cdada76651a8391a99bbf3966 [sid] Package: ariba Source: ariba (2.14.7+ds-7) Version: 2.14.7+ds-7+b1 Installed-Size: 20464 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.14), python3 (>= 3.13~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-pkg-resources, python3-tk Suggests: spades Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-7+b1_amd64.deb Size: 1957104 MD5sum: 3348702bfb562eb4a668ae314db3262e SHA256: 62ebed4b7a7a87096ad19c18ef32637ce1ae003a29841d801fce658d7398229f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt ariba=2.14.7+ds-7+b1 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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt ariba=2.14.7+ds-7+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpcn0n5hm0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpcn0n5hm0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpcn0n5hm0/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'update'] 0m1.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9689 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6498 kB] Fetched 16.4 MB in 1s (21.3 MB/s) Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash bsdutils debian-archive-keyring debianutils libblkid1 libcap2 liblastlog2-2 libmount1 libsmartcols1 libsqlite3-0 libuuid1 login mount perl-base tzdata util-linux 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6843 kB of archives. After this operation, 70.7 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.22 [92.2 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-2 [1500 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.41-4 [110 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.40.1-3 [1665 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 liblastlog2-2 amd64 2.41-4 [28.4 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.41-4 [37.6 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.41-4 [171 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.41-4 [209 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.41-4 [143 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.41-4 [1234 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.41-4 [162 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-3 [913 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.41-4 [112 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 debian-archive-keyring all 2025.1 [179 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.75-6 [28.0 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-2 [260 kB] Preconfiguring packages ... Fetched 6843 kB in 0s (171 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 ... 4927 files and directories currently installed.) Preparing to unpack .../debianutils_5.22_amd64.deb ... Unpacking debianutils (5.22) over (5.21) ... Setting up debianutils (5.22) ... (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 ... 4927 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-2_amd64.deb ... Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ... Setting up bash (5.2.37-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 4926 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.41-4_amd64.deb ... Unpacking bsdutils (1:2.41-4) over (1:2.41-3) ... Setting up bsdutils (1:2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../perl-base_5.40.1-3_amd64.deb ... Unpacking perl-base (5.40.1-3) over (5.40.1-2) ... Setting up perl-base (5.40.1-3) ... (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 ... 4926 files and directories currently installed.) Preparing to unpack .../liblastlog2-2_2.41-4_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41-4) over (2.41-3) ... Setting up liblastlog2-2:amd64 (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libuuid1_2.41-4_amd64.deb ... Unpacking libuuid1:amd64 (2.41-4) over (2.41-3) ... Setting up libuuid1:amd64 (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libblkid1_2.41-4_amd64.deb ... Unpacking libblkid1:amd64 (2.41-4) over (2.41-3) ... Setting up libblkid1:amd64 (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libmount1_2.41-4_amd64.deb ... Unpacking libmount1:amd64 (2.41-4) over (2.41-3) ... Setting up libmount1:amd64 (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.41-4_amd64.deb ... Unpacking libsmartcols1:amd64 (2.41-4) over (2.41-3) ... Setting up libsmartcols1:amd64 (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../util-linux_2.41-4_amd64.deb ... Unpacking util-linux (2.41-4) over (2.41-3) ... Setting up util-linux (2.41-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../mount_2.41-4_amd64.deb ... Unpacking mount (2.41-4) over (2.41-3) ... Preparing to unpack .../libsqlite3-0_3.46.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-3) over (3.46.1-2) ... Setting up libsqlite3-0:amd64 (3.46.1-3) ... (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 ... 4926 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.41-4_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41-4) over (1:4.16.0-2+really2.41-3) ... Preparing to unpack .../debian-archive-keyring_2025.1_all.deb ... Unpacking debian-archive-keyring (2025.1) over (2023.4) ... Setting up debian-archive-keyring (2025.1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.asc ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.asc ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.asc ... (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 ... 4938 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.75-6_amd64.deb ... Unpacking libcap2:amd64 (1:2.75-6) over (1:2.75-4) ... Setting up libcap2:amd64 (1:2.75-6) ... (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 ... 4938 files and directories currently installed.) Preparing to unpack .../tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) over (2025b-1) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Apr 16 03:30:51 UTC 2025. Universal Time is now: Wed Apr 16 03:30:51 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mount (2.41-4) ... Setting up login (1:4.16.0-2+really2.41-4) ... Processing triggers for debianutils (5.22) ... Processing triggers for libc-bin (2.41-6) ... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s DUMP: a25703f1db8760d5ffc0df7e88d5a932 - 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s INFO: Running scripts post_setup 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s 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 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-6 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl-base perl-base 5.40.1-3 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m3.7s INFO: Running scripts is_testable 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/is_testable_uninstallable'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/is_testable_uninstallable'] 0m3.7s INFO: Running scripts pre_test 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_test_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_test_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_test_root_password'] 0m3.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_test_root_password'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m3.9s DUMP: Package: ariba Version: 2.14.7+ds-7 Installed-Size: 20596 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.14), python3 (>= 3.12~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-pkg-resources, python3-tk Suggests: spades Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-7_amd64.deb Size: 1957620 MD5sum: 35d5f2dd2bc36825173336d5988a649d SHA256: 8f5128a7633fcc13c4677f4ab6de6d8311df028cdada76651a8391a99bbf3966 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m3.9s INFO: apt-cache knows about the following packages: ariba 0m3.9s INFO: Running scripts pre_install 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m3.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m3.9s DUMP: ariba: Installed: (none) Candidate: 2.14.7+ds-7 Version table: 2.14.7+ds-7 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba'] 0m40.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 gawk libatomic1 libblas3 libbrotli1 libcairo2 libcapnp-1.1.0 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfml0 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libminimap0 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsigsegv2 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzopfli1 mash media-types mummer netbase perl perl-modules-5.40 python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dendropy python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13 python3.13-minimal python3.13-tk readline-common samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: spades blt-demo bowtie2-examples fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gawk-doc rng-tools gdbm-l10n low-memory-monitor gnutls-bin gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils sensible-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 python3-igraph raxml t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 gir1.2-gtk-4.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc binutils binfmt-support readline-doc cwltool sgml-base-doc debhelper Recommended packages: ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-cssselect python3-html5lib python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch python3-yaml isympy-common The following NEW packages will be installed: ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 gawk libatomic1 libblas3 libbrotli1 libcairo2 libcapnp-1.1.0 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfml0 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libminimap0 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsigsegv2 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzopfli1 mash media-types mummer netbase perl perl-modules-5.40 python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dendropy python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13 python3.13-minimal python3.13-tk readline-common samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 133 MB of archives. After this operation, 537 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libsigsegv2 amd64 2.14-1+b2 [34.4 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-3 [861 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-3 [2212 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-3 [1952 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-3 [746 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.1-3 [3021 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-3 [4320 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-3 [267 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:39 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 fastaq all 3.17.0-9 [47.8 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:69 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.2-3 [107 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get:84 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.13.3-1 [9548 B] Get:85 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:93 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-4 [1672 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.13.0-1 [90.1 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-bs4 all 4.13.3-2 [166 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.10.1+dfsg1-2 [2736 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-7 [95.2 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.2 [233 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.2-1 [1297 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-2 [25.3 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-5 [4148 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b4 [299 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.57.0-1 [1438 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-2 [23.8 MB] Get:152 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 python3-pymummer all 0.11.0-5 [18.1 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libfml0 amd64 0.1+git20221215.85f159e-1 [70.1 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libminimap0 amd64 0.2-8+b3 [22.7 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.4-1+b2 [1505 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1479 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libmurmurhash2 amd64 1.6-1+b1 [6180 B] Get:163 http://deb.debian.org/debian trixie/main amd64 mash amd64 2.3+dfsg-6+b2 [192 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:169 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 ariba amd64 2.14.7+ds-7 [1958 kB] Preconfiguring packages ... Fetched 133 MB in 1s (165 MB/s) Selecting previously unselected package libmpfr6: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 ... 4942 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.2.2-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.2.2-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b2) ... Setting up libmpfr6:amd64 (4.2.2-1) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libsigsegv2:amd64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 4996 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-3_amd64.deb ... 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Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1+b1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libfml0:amd64 (0.1+git20221215.85f159e-1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up unicode-data (15.1.0-1) ... Setting up libminimap0:amd64 (0.2-8+b3) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up perl-modules-5.40 (5.40.1-3) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up sgml-base (1.31) ... Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up python-matplotlib-data (3.10.1+dfsg1-2) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-3) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.13.2-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up python3.13 (3.13.2-3) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up python3 (3.13.2-2) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.7-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up python3-fs (2.4.16-7) ... Setting up libperl5.40:amd64 (5.40.1-3) ... Setting up python3-decorator (5.1.1-5) ... Setting up perl (5.40.1-3) ... Setting up libglib2.0-0t64:amd64 (2.84.1-1) ... No schema files found: doing nothing. Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up python3-cycler (0.12.1-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up mash (2.3+dfsg-6+b2) ... Setting up python3-typing-extensions (4.13.0-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.2) ... Setting up mummer (3.23+dfsg-8) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-dendropy (4.6.1-2) ... 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Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-lxml:amd64 (5.3.2-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-cairo (1.27.0-2) ... Setting up blt (2.5.3+dfsg-8) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-1) ... Setting up python3-tk:amd64 (3.13.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.3.1-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up samtools (1.21-1) ... Setting up fastaq (3.17.0-9) ... Setting up python3-pymummer (0.11.0-5) ... Setting up python3-fonttools (4.57.0-1) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-2) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-4) ... Setting up ariba (2.14.7+ds-7) ... 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba'] 0m40.6s INFO: Running scripts post_install 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m40.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m41.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m41.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpcn0n5hm0 to sid 0m41.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m41.3s INFO: Running scripts pre_distupgrade 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'update'] 0m43.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7422 kB] Fetched 17.8 MB in 1s (13.0 MB/s) Reading package lists... 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'update'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-yf', 'dist-upgrade'] 0m49.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: ariba coreutils libc-bin libc6 libcurl3t64-gnutls libdebconfclient0 libdeflate0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib python3 python3-decorator python3-minimal python3-packaging python3-pkg-resources python3-scipy python3-typing-extensions python3.13 python3.13-minimal python3.13-tk 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 31.6 MB of archives. After this operation, 352 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.41-7 [2847 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.41-7 [636 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.3-2 [751 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.3-2 [2212 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.3-2 [861 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.3-2 [1953 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 78.1.0-1.1 [224 kB] Get:13 http://deb.debian.org/debian sid/main amd64 ariba amd64 2.14.7+ds-7+b1 [1957 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.13.0-2 [374 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.2.1-1 [32.9 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-3 [55.7 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.15.2-8 [16.3 MB] Get:19 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.3-2 [107 kB] Preconfiguring packages ... Fetched 31.6 MB in 0s (167 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 ... 22661 files and directories currently installed.) Preparing to unpack .../coreutils_9.7-1_amd64.deb ... Unpacking coreutils (9.7-1) over (9.5-1+b1) ... Setting up coreutils (9.7-1) ... (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 ... 22660 files and directories currently installed.) Preparing to unpack .../libc6_2.41-7_amd64.deb ... Unpacking libc6:amd64 (2.41-7) over (2.41-6) ... Setting up libc6:amd64 (2.41-7) ... (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 ... 22660 files and directories currently installed.) Preparing to unpack .../libc-bin_2.41-7_amd64.deb ... Unpacking libc-bin (2.41-7) over (2.41-6) ... Setting up libc-bin (2.41-7) ... (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 ... 22660 files and directories currently installed.) Preparing to unpack .../python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) over (3.13.2-3) ... Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) over (3.13.2-3) ... Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) over (3.13.2-3) ... Preparing to unpack .../libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) over (3.13.2-3) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up python3.13-minimal (3.13.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22661 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) over (3.13.2-2) ... Setting up python3-minimal (3.13.3-1) ... (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 ... 22661 files and directories currently installed.) Preparing to unpack .../python3_3.13.3-1_amd64.deb ... Unpacking python3 (3.13.3-1) over (3.13.2-2) ... Preparing to unpack .../libpython3-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.3-1) over (3.13.2-2) ... Preparing to unpack .../libdebconfclient0_0.278_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.278) over (0.277) ... Setting up libdebconfclient0:amd64 (0.278) ... (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 ... 22661 files and directories currently installed.) Preparing to unpack .../0-python3-pkg-resources_78.1.0-1.1_all.deb ... Unpacking python3-pkg-resources (78.1.0-1.1) over (75.8.0-1) ... Preparing to unpack .../1-ariba_2.14.7+ds-7+b1_amd64.deb ... Unpacking ariba (2.14.7+ds-7+b1) over (2.14.7+ds-7) ... Preparing to unpack .../2-libcurl3t64-gnutls_8.13.0-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.13.0-2) over (8.13.0-1) ... Preparing to unpack .../3-libdeflate0_1.23-2_amd64.deb ... Unpacking libdeflate0:amd64 (1.23-2) over (1.23-1+b1) ... Preparing to unpack .../4-python3-decorator_5.2.1-1_all.deb ... Unpacking python3-decorator (5.2.1-1) over (5.1.1-5) ... Preparing to unpack .../5-python3-packaging_24.2-3_all.deb ... Unpacking python3-packaging (24.2-3) over (24.2-1) ... Preparing to unpack .../6-python3-scipy_1.15.2-8_amd64.deb ... Unpacking python3-scipy (1.15.2-8) over (1.15.2-7) ... Preparing to unpack .../7-python3-typing-extensions_4.13.2-1_all.deb ... Unpacking python3-typing-extensions (4.13.2-1) over (4.13.0-1) ... Preparing to unpack .../8-python3.13-tk_3.13.3-2_amd64.deb ... Unpacking python3.13-tk (3.13.3-2) over (3.13.2-3) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-2) ... Setting up python3.13-tk (3.13.3-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up python3 (3.13.3-1) ... Setting up python3-decorator (5.2.1-1) ... Setting up python3-packaging (24.2-3) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up python3-pkg-resources (78.1.0-1.1) ... Setting up ariba (2.14.7+ds-7+b1) ... Setting up python3-scipy (1.15.2-8) ... Processing triggers for libc-bin (2.41-7) ... 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-yf', 'dist-upgrade'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.3s DUMP: 61b114a4debf2a35acedd4bffbfdc34a - 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m49.4s DUMP: Package: ariba Source: ariba (2.14.7+ds-7) Version: 2.14.7+ds-7+b1 Installed-Size: 20464 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.14), python3 (>= 3.13~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-pkg-resources, python3-tk Suggests: spades Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-7+b1_amd64.deb Size: 1957104 MD5sum: 3348702bfb562eb4a668ae314db3262e SHA256: 62ebed4b7a7a87096ad19c18ef32637ce1ae003a29841d801fce658d7398229f 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m49.4s INFO: apt-cache knows about the following packages: ariba 0m49.4s INFO: Running scripts pre_install 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m49.5s 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: 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m49.5s DUMP: ariba: Installed: 2.14.7+ds-7+b1 Candidate: 2.14.7+ds-7+b1 Version table: *** 2.14.7+ds-7+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba'] 0m49.8s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.14.7+ds-7+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba'] 0m49.8s INFO: Running scripts post_install 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m49.8s INFO: Running scripts post_distupgrade 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_exceptions'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_exceptions'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m49.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m50.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m50.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m51.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m51.4s INFO: Running scripts pre_install 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_database-server'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_exceptions'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_extras'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m51.5s 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: 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m51.5s DUMP: ariba: Installed: 2.14.7+ds-7+b1 Candidate: 2.14.7+ds-7+b1 Version table: *** 2.14.7+ds-7+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-cache', 'policy', 'ariba'] 0m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba=2.14.7+ds-7+b1'] 0m51.8s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.14.7+ds-7+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', '-y', 'install', 'ariba=2.14.7+ds-7+b1'] 0m51.8s INFO: Running scripts post_install 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_install_exceptions'] 0m51.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m52.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 0m53.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', '-ac', '--ignore-obsolete'] 0m55.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', '-ac', '--ignore-obsolete'] 0m55.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m55.0s DUMP: 0.15.6 0m55.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m55.0s INFO: Running adequate version 0.15.6 now. 0m55.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'ariba'] 0m55.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'ariba'] 0m55.1s INFO: Running scripts pre_remove 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_exceptions'] 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/pre_remove_exceptions'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m56.7s DUMP: install ok installed apt apt 3.0.0 install ok installed ariba ariba 2.14.7+ds-7+b1 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed blt blt 2.5.3+dfsg-8 install ok installed bowtie2 bowtie2 2.5.4-1+b2 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.7-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed fastaq fastaq 3.17.0-9 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-2.3 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.3-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gawk gawk 1:5.2.1-2+b1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.41-4 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-7 install ok installed libc6:amd64 libc6 2.41-7 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-6 install ok installed libcapnp-1.1.0:amd64 libcapnp-1.1.0 1.1.0-2 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.13.0-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libdeflate0:amd64 libdeflate0 1.23-2 install ok installed libexpat1:amd64 libexpat1 2.7.1-1 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfml0:amd64 libfml0 0.1+git20221215.85f159e-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgsl28:amd64 libgsl28 2.8+dfsg-5 install ok installed libgslcblas0:amd64 libgslcblas0 2.8+dfsg-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libminimap0:amd64 libminimap0 0.2-8+b3 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libmpfr6:amd64 libmpfr6 4.2.2-1 install ok installed libmurmurhash2:amd64 libmurmurhash2 1.6-1+b1 install ok installed libncurses6:amd64 libncurses6 6.5+20250216-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.3-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.3-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.3-2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.2 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzopfli1 libzopfli1 1.0.3-3 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mash mash 2.3+dfsg-6+b2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mount mount 2.41-4 install ok installed mummer mummer 3.23+dfsg-8 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl perl 5.40.1-3 install ok installed perl-base perl-base 5.40.1-3 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-3 install ok installed python-matplotlib-data python-matplotlib-data 3.10.1+dfsg1-2 install ok installed python3 python3 3.13.3-1 install ok installed python3-attr python3-attr 25.3.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.85+dfsg-4 install ok installed python3-brotli python3-brotli 1.1.0-2+b7 install ok installed python3-bs4 python3-bs4 4.13.3-2 install ok installed python3-cairo python3-cairo 1.27.0-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-contourpy python3-contourpy 1.3.1-1+b1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-decorator python3-decorator 5.2.1-1 install ok installed python3-dendropy python3-dendropy 4.6.1-2 install ok installed python3-fonttools python3-fonttools 4.57.0-1 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-7 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.1-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3+b1 install ok installed python3-lxml:amd64 python3-lxml 5.3.2-1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-2 install ok installed python3-matplotlib python3-matplotlib 3.10.1+dfsg1-2 install ok installed python3-minimal python3-minimal 3.13.3-1 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-packaging python3-packaging 24.2-3 install ok installed python3-pil:amd64 python3-pil 11.1.0-5+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5+b1 install ok installed python3-pkg-resources python3-pkg-resources 78.1.0-1.1 install ok installed python3-platformdirs python3-platformdirs 4.3.7-1 install ok installed python3-pymummer python3-pymummer 0.11.0-5 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1 install ok installed python3-reportlab python3-reportlab 4.3.1-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.15.2-8 install ok installed python3-soupsieve python3-soupsieve 2.6-1 install ok installed python3-sympy python3-sympy 1.13.3-5 install ok installed python3-tk:amd64 python3-tk 3.13.3-1 install ok installed python3-typeguard python3-typeguard 4.4.2-1 install ok installed python3-typing-extensions python3-typing-extensions 4.13.2-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b4 install ok installed python3-zopfli python3-zopfli 0.2.3.post1-1+b1 install ok installed python3.13 python3.13 3.13.3-2 install ok installed python3.13-minimal python3.13-minimal 3.13.3-2 install ok installed python3.13-tk python3.13-tk 3.13.3-2 install ok installed readline-common readline-common 8.2-6 install ok installed samtools samtools 1.21-1 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-8 install ok installed tzdata tzdata 2025b-2 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'bowtie2', 'cd-hit', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libminimap0:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libzopfli1', 'mash', 'media-types', 'mummer', 'netbase', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-zopfli', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'samtools', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'ariba'] 1m16.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 gawk libatomic1 libblas3 libbrotli1 libcairo2 libcapnp-1.1.0 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfml0 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgsl28 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libminimap0 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsigsegv2 libssh2-1t64 libtasn1-6 libtcl8.6 libtiff6 libtk8.6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libzopfli1 mash media-types mummer netbase perl perl-modules-5.40 python-matplotlib-data python3 python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dendropy python3-fonttools python3-freetype python3-fs python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13 python3.13-minimal python3.13-tk readline-common samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 171 to remove and 0 not upgraded. After this operation, 537 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 22659 files and directories currently installed.) Removing ariba (2.14.7+ds-7+b1) ... Removing python3-biopython (1.85+dfsg-4) ... Removing python3-reportlab (4.3.1-1) ... Removing python3-matplotlib (3.10.1+dfsg1-2) ... Removing python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Removing python3-pil:amd64 (11.1.0-5+b1) ... Removing python3-tk:amd64 (3.13.3-1) ... Removing blt (2.5.3+dfsg-8) ... Removing bowtie2 (2.5.4-1+b2) ... Removing cd-hit (4.8.1-4) ... Removing python3-pymummer (0.11.0-5) ... Removing fastaq (3.17.0-9) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-8) ... Removing python3.13-tk (3.13.3-2) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.27.0-2) ... Removing libcairo2:amd64 (1.18.4-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-2.3) ... Removing fontconfig-config (2.15.0-2.3) ... Removing python-matplotlib-data (3.10.1+dfsg1-2) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.3-1) ... Removing fonts-urw-base35 (20200910-8) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2+b1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libglib2.0-0t64:amd64 (2.84.1-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing python3-contourpy (1.3.1-1+b1) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing samtools (1.21-1) ... Removing mash (2.3+dfsg-6+b2) ... Removing libcapnp-1.1.0:amd64 (1.1.0-2) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing python3-pkg-resources (78.1.0-1.1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.2-1) ... Removing python3-bs4 (4.13.3-2) ... Removing python3-soupsieve (2.6-1) ... Removing python3-jaraco.context (6.0.1-1) ... Removing libfml0:amd64 (0.1+git20221215.85f159e-1) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing perl (5.40.1-3) ... Removing libperl5.40:amd64 (5.40.1-3) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libgsl28:amd64 (2.8+dfsg-5) ... Removing libgslcblas0:amd64 (2.8+dfsg-5) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libminimap0:amd64 (0.2-8+b3) ... Removing libmpfr6:amd64 (4.2.2-1) ... Removing libmurmurhash2:amd64 (1.6-1+b1) ... Removing libncurses6:amd64 (6.5+20250216-2) ... Removing libopenjp2-7:amd64 (2.5.3-2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.47-1.1) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libsigsegv2:amd64 (2.14-1+b2) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing perl-modules-5.40 (5.40.1-3) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-4) ... Removing python3-dendropy (4.6.1-2) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-kiwisolver (1.4.7-3+b1) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-packaging (24.2-3) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-pysam (0.23.0+ds-1+b1) ... Removing python3-typing-extensions (4.13.2-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.13.0-2) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-1+b1) ... Removing libdeflate0:amd64 (1.23-2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-6) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing libldap2:amd64 (2.6.9+dfsg-2) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing libgnutls30t64:amd64 (3.8.9-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-2) ... Removing python3-ufolib2 (0.17.1+dfsg1-1) ... Removing python3-attr (25.3.0-1) ... Removing python3-fonttools (4.57.0-1) ... Removing python3-scipy (1.15.2-8) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3-zopfli (0.2.3.post1-1+b1) ... Removing python3-sympy (1.13.3-5) ... Removing python3-unicodedata2 (15.1.0+ds-1+b4) ... Removing python3-lxml:amd64 (5.3.2-1) ... Removing libxslt1.1:amd64 (1.1.35-1.2) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libgpg-error0:amd64 (1.51-4) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Removing libzopfli1 (1.0.3-3) ... Removing python3-brotli (1.1.0-2+b7) ... Removing python3-decorator (5.2.1-1) ... Removing python3-fs (2.4.16-7) ... Removing python3-lz4 (4.4.0+dfsg-2) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing python3-platformdirs (4.3.7-1) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.13.3-1) ... Removing python3.13 (3.13.3-2) ... Removing python3-minimal (3.13.3-1) ... Removing python3.13-minimal (3.13.3-2) ... Removing libexpat1:amd64 (2.7.1-1) ... Removing libpython3-stdlib:amd64 (3.13.3-1) ... Removing libpython3.13-stdlib:amd64 (3.13.3-2) ... find: '/usr/lib/python3': No such file or directory Removing libffi8:amd64 (3.4.7-1) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libpython3.13-minimal:amd64 (3.13.3-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... 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 media-types (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-7) ... 1m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'remove', '--allow-remove-essential', 'blt', 'bowtie2', 'cd-hit', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libminimap0:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libzopfli1', 'mash', 'media-types', 'mummer', 'netbase', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-zopfli', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'samtools', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'ariba'] 1m16.7s INFO: Running scripts post_remove 1m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_remove_exceptions'] 1m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_remove_exceptions'] 1m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', 'blt', 'bowtie2', 'cd-hit', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libminimap0:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libzopfli1', 'mash', 'media-types', 'mummer', 'netbase', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-zopfli', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'samtools', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m16.9s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed (Reading database ... 5004 files and directories currently installed.) Purging configuration files for fontconfig-config (2.15.0-2.3) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... Purging configuration files for gawk (1:5.2.1-2+b1) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-1.1.0 which isn't installed dpkg: warning: ignoring request to remove libcom-err2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libfml0 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcrypt20 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.84.1-1) ... dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpg-error0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl28 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libminimap0 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmurmurhash2 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 libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.3-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libzopfli1 which isn't installed dpkg: warning: ignoring request to remove mash which isn't installed Purging configuration files for media-types (13.0.0) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for netbase (6.5) ... Purging configuration files for perl (5.40.1-3) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python-matplotlib-data (3.10.1+dfsg1-2) ... Purging configuration files for python3 (3.13.3-1) ... dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-bs4 which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed Purging configuration files for python3-numpy (1:2.2.4+ds-1) ... dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pymummer which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-soupsieve which isn't installed Purging configuration files for python3-sympy (1.13.3-5) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-zopfli which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.3-2) ... dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-6) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.31) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', 'blt', 'bowtie2', 'cd-hit', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'gawk', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcapnp-1.1.0:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcrypt20:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgsl28:amd64', 'libgslcblas0:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libminimap0:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libzopfli1', 'mash', 'media-types', 'mummer', 'netbase', 'perl', 'perl-modules-5.40', 'python-matplotlib-data', 'python3', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-ufolib2', 'python3-unicodedata2', 'python3-zopfli', 'python3.13', 'python3.13-minimal', 'python3.13-tk', 'readline-common', 'samtools', 'sgml-base', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', 'ariba'] 1m16.9s DUMP: dpkg: warning: ignoring request to remove ariba which isn't installed 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', 'ariba'] 1m16.9s INFO: Running scripts post_purge 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_purge_exceptions'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_purge_exceptions'] 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', '--pending'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--purge', '--pending'] 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--remove', '--pending'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg', '--remove', '--pending'] 1m16.9s INFO: Running scripts post_test 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_test_exceptions'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'tmp/scripts/post_test_exceptions'] 1m16.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 1m17.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 1m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-divert', '--list'] 1m17.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'dpkg-divert', '--list'] 1m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'clean'] 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0', 'apt-get', 'clean'] 1m17.2s DEBUG: Recording chroot state 1m17.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/shm'] 1m17.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/shm'] 1m17.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/console'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/console'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/ptmx'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/ptmx'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/dev/pts'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/proc'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0/proc'] 1m17.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 1m17.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcn0n5hm0'] 1m17.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpcn0n5hm0 1m17.9s INFO: PASS: Upgrading between Debian distributions. 1m17.9s INFO: PASS: All tests. 1m17.9s INFO: piuparts run ends. ret=0 End: 2025-04-16 03:32:06 GMT