Start: 2025-08-12 12:58:54 GMT [trixie] Package: seqsero Version: 1.0.1+dfsg-6 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description: Salmonella serotyping from genome sequencing data Homepage: https://github.com/denglab/SeqSero Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-6_amd64.deb Size: 358116 MD5sum: 744848c9c6bb706b8e3cb96375e6edb2 SHA256: 042f2f1e7f49abb9360a13f2443acfd2318dd331cb2a7cb494fa7dcb26713ad6 [trixie-next] Package: seqsero Version: 1.0.1+dfsg-6 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description: Salmonella serotyping from genome sequencing data Homepage: https://github.com/denglab/SeqSero Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-6_amd64.deb Size: 358116 MD5sum: 744848c9c6bb706b8e3cb96375e6edb2 SHA256: 042f2f1e7f49abb9360a13f2443acfd2318dd331cb2a7cb494fa7dcb26713ad6 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-6 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 1.6.1~202508101417~1.6.0-7-g17c4ea32 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp3se8ggqo 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp3se8ggqo 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', '--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/tmp3se8ggqo', '--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/tmp3se8ggqo/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/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/tmp3se8ggqo/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/tmp3se8ggqo/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/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/tmp3se8ggqo/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'update'] 0m1.3s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (14.7 MB/s) Reading package lists... 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'update'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-yf', 'dist-upgrade'] 0m1.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-yf', 'dist-upgrade'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s INFO: Running scripts post_setup 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_dummy_users'] 0m2.2s 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 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_dummy_users'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_forbid_home'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s 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' 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_minimize'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_minimize'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_zz_backports'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_setup_zz_backports'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.3s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 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 3.0.3 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 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 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 0.280 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 2.41-5 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 libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 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 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 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+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 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 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 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-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m2.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m2.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m2.5s INFO: Running scripts is_testable 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/is_testable_uninstallable'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/is_testable_uninstallable'] 0m2.5s INFO: Running scripts pre_test 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_test_exceptions'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_test_exceptions'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_test_root_password'] 0m2.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_test_root_password'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m2.6s DUMP: Package: seqsero Version: 1.0.1+dfsg-6 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description-en: Salmonella serotyping from genome sequencing data SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. . SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing 1. raw reads from genomes of 308 Salmonella isolates of known serotype 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and 3. 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Homepage: https://github.com/denglab/SeqSero Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-6_amd64.deb Size: 358116 MD5sum: 744848c9c6bb706b8e3cb96375e6edb2 SHA256: 042f2f1e7f49abb9360a13f2443acfd2318dd331cb2a7cb494fa7dcb26713ad6 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m2.6s INFO: apt-cache knows about the following packages: seqsero 0m2.6s INFO: Running scripts pre_install 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m2.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m2.7s DUMP: seqsero: Installed: (none) Candidate: 1.0.1+dfsg-6 Version table: 1.0.1+dfsg-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero'] 0m29.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libabsl20240722 libaec0 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libcurl4t64 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-310 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libre2-11 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libsz2 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 media-types ncbi-vdb-data netbase python3 python3-biopython python3-cairo python3-chardet python3-freetype python3-minimal python3-numpy python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 python3.13-minimal readline-common samtools sgml-base sra-toolkit w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre low-memory-monitor gnutls-bin krb5-doc krb5-user liblcms2-utils file python3-doc python3-tk python3-venv clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy python3-igraph raxml t-coffee wise gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc binutils binfmt-support readline-doc cwltool ispcr sgml-base-doc debhelper Recommended packages: perl ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra med-config The following NEW packages will be installed: bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libabsl20240722 libaec0 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libcurl4t64 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-310 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libre2-11 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libsz2 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 media-types ncbi-vdb-data netbase python3 python3-biopython python3-cairo python3-chardet python3-freetype python3-minimal python3-numpy python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 python3.13-minimal readline-common samtools seqsero sgml-base sra-toolkit w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 115 newly installed, 0 to remove and 0 not upgraded. Need to get 60.7 MB of archives. After this operation, 203 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-6 [160 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-6 [2447 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.18-1 [212 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:31 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:35 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:56 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get:77 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libncbi-wvdb3 amd64 3.2.1+dfsg-2 [1167 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libre2-11 amd64 20240702-3+b1 [169 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 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 python3-cairo amd64 1.27.0-2 [114 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.85+dfsg-4 [1672 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.21-1 [667 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 sra-toolkit amd64 3.2.1+dfsg-4 [7232 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 seqsero amd64 1.0.1+dfsg-6 [358 kB] Preconfiguring packages ... 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Preparing to unpack .../099-samtools_1.21-1_amd64.deb ... Unpacking samtools (1.21-1) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../100-sra-toolkit_3.2.1+dfsg-4_amd64.deb ... Unpacking sra-toolkit (3.2.1+dfsg-4) ... Selecting previously unselected package seqsero. Preparing to unpack .../101-seqsero_1.0.1+dfsg-6_amd64.deb ... Unpacking seqsero (1.0.1+dfsg-6) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up media-types (13.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up bwa (0.7.18-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... 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 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-6) ... 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 (1:2.1.5-4) ... 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 (1.6.48-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... 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 (3.4.8-2) ... 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 ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up sgml-base (1.31+nmu1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libre2-11:amd64 (20240702-3+b1) ... Setting up liblapack3:amd64 (3.12.1-6) ... 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 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 libidn2-0:amd64 (2.3.8-2) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up python3.13 (3.13.5-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.5-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up python3-cairo (1.27.0-2) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.3.1-1) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up sra-toolkit (3.2.1+dfsg-4) ... Setting up samtools (1.21-1) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-4) ... Setting up seqsero (1.0.1+dfsg-6) ... 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero'] 0m29.6s INFO: Running scripts post_install 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m29.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m30.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m30.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3se8ggqo to trixie-next 0m30.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m30.0s INFO: Running scripts pre_distupgrade 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'update'] 0m30.6s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://security.debian.org trixie-security InRelease [43.4 kB] Get:3 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:4 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:5 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:6 http://security.debian.org trixie-security/main Translation-en [6724 B] Get:7 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:8 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:9 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:10 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Fetched 172 kB in 0s (1061 kB/s) Reading package lists... 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'update'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-yf', 'dist-upgrade'] 0m30.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-yf', 'dist-upgrade'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m31.1s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m31.2s DUMP: Package: seqsero Version: 1.0.1+dfsg-6 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, python3-biopython, bwa, samtools, sra-toolkit Suggests: ispcr Description-en: Salmonella serotyping from genome sequencing data SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. . SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing 1. raw reads from genomes of 308 Salmonella isolates of known serotype 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and 3. 354 other publicly available draft or complete Salmonella genomes. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization. Description-md5: 8a40b6660777f02ab6eed37f09c29dc5 Homepage: https://github.com/denglab/SeqSero Section: science Priority: optional Filename: pool/main/s/seqsero/seqsero_1.0.1+dfsg-6_amd64.deb Size: 358116 MD5sum: 744848c9c6bb706b8e3cb96375e6edb2 SHA256: 042f2f1e7f49abb9360a13f2443acfd2318dd331cb2a7cb494fa7dcb26713ad6 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m31.2s INFO: apt-cache knows about the following packages: seqsero 0m31.2s INFO: Running scripts pre_install 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m31.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m31.3s DUMP: seqsero: Installed: 1.0.1+dfsg-6 Candidate: 1.0.1+dfsg-6 Version table: *** 1.0.1+dfsg-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero'] 0m31.5s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero'] 0m31.5s INFO: Running scripts post_install 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m31.5s INFO: Running scripts post_distupgrade 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_exceptions'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_exceptions'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m31.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m31.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m31.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m32.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m32.3s INFO: Running scripts pre_install 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_database-server'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_exceptions'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_extras'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m32.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m32.4s DUMP: seqsero: Installed: 1.0.1+dfsg-6 Candidate: 1.0.1+dfsg-6 Version table: *** 1.0.1+dfsg-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-cache', 'policy', 'seqsero'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 0m32.6s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 0m32.6s INFO: Running scripts post_install 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_install_exceptions'] 0m32.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m33.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m33.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', '-ac', '--ignore-obsolete'] 0m34.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', '-ac', '--ignore-obsolete'] 0m34.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m34.1s DUMP: 0.15.9~deb12u1 0m34.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m34.1s INFO: Running adequate version 0.15.9~deb12u1 now. 0m34.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'seqsero'] 0m34.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'seqsero'] 0m34.2s INFO: Running scripts pre_remove 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_exceptions'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/pre_remove_exceptions'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.0s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed bwa bwa 0.7.18-1 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 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-urw-base35 fonts-urw-base35 20200910-8 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 libabsl20240722:amd64 libabsl20240722 20240722.0-4 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libaec0:amd64 libaec0 1.1.3-1+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 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 3.12.1-6 install ok installed libblkid1:amd64 libblkid1 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 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 1:2.75-10+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-3+b3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.14.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.14.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdeflate0:amd64 libdeflate0 1.23-2 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.4.8-2 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 libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.3-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhdf5-310:amd64 libhdf5-310 1.14.5+repack-3 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 1:2.1.5-4 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 3.12.1-6 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.10+dfsg-1 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 libmagic-mgc libmagic-mgc 1:5.46-5 install ok installed libmagic1t64:amd64 libmagic1t64 1:5.46-5 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.4-2 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.4-2 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.4-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libncbi-wvdb3:amd64 libncbi-wvdb3 3.2.1+dfsg-2 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 1.64.0-1.1 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 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.48-1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.5-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.5-2 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libre2-11:amd64 libre2-11 20240702-3+b1 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 libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libsz2:amd64 libsz2 1.1.3-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-5 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 libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-2.1 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 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+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 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 2.41-5 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 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 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed python3 python3 3.13.5-1 install ok installed python3-biopython python3-biopython 1.85+dfsg-4 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-freetype python3-freetype 2.5.1-1 install ok installed python3-minimal python3-minimal 3.13.5-1 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-pil:amd64 python3-pil 11.1.0-5+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 python3.13 python3.13 3.13.5-2 install ok installed python3.13-minimal python3.13-minimal 3.13.5-2 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 seqsero seqsero 1.0.1+dfsg-6 install ok installed sgml-base sgml-base 1.31+nmu1 install ok installed sqv sqv 1.3.0-3 install ok installed sra-toolkit sra-toolkit 3.2.1+dfsg-4 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-4 install ok installed util-linux util-linux 2.41-5 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 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'remove', '--allow-remove-essential', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libaec0:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-310:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libre2-11:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libtiff6: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', 'libxml2:amd64', 'libxrender1:amd64', 'media-types', 'ncbi-vdb-data', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-reportlab', 'python3-rlpycairo', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 0m54.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bwa fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libabsl20240722 libaec0 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libcurl4t64 libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-310 libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libre2-11 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libsz2 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 media-types ncbi-vdb-data netbase python3 python3-biopython python3-cairo python3-chardet python3-freetype python3-minimal python3-numpy python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 python3.13-minimal readline-common samtools seqsero sgml-base sra-toolkit w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 115 to remove and 0 not upgraded. After this operation, 203 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 ... 10494 files and directories currently installed.) Removing seqsero (1.0.1+dfsg-6) ... Removing bwa (0.7.18-1) ... Removing python3-biopython (1.85+dfsg-4) ... Removing python3-reportlab (4.3.1-1) ... 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 fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-8) ... Removing sra-toolkit (3.2.1+dfsg-4) ... Removing libre2-11:amd64 (20240702-3+b1) ... Removing libabsl20240722:amd64 (20240722.0-4) ... Removing libhdf5-310:amd64 (1.14.5+repack-3) ... Removing libsz2:amd64 (1.1.3-1+b1) ... Removing libaec0:amd64 (1.1.3-1+b1) ... Removing python3-pil:amd64 (11.1.0-5+b1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libglib2.0-0t64:amd64 (2.84.3-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-6) ... Removing libblas3:amd64 (3.12.1-6) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.14.1-2) ... Removing samtools (1.21-1) ... Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.14.1-2) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-3+b3) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-2) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3 (3.13.5-1) ... Removing python3.13 (3.13.5-2) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13-minimal (3.13.5-2) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.5-2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libgfortran5:amd64 (14.2.0-19) ... 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 libhtscodecs2:amd64 (1.6.1-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-4) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-6) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.10+dfsg-1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libmagic1t64:amd64 (1:5.46-5) ... Removing libmagic-mgc (1:5.46-5) ... Removing libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.4-2) ... Removing libmbedx509-7:amd64 (3.6.4-2) ... Removing libncurses6:amd64 (6.5+20250216-2) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1) ... 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 libopenjp2-7:amd64 (2.5.3-2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.48-1) ... Removing libpython3.13-minimal:amd64 (3.13.5-2) ... 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 libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... 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 libssh2-1t64:amd64 (1.11.1-1) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... 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 libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Removing media-types (13.0.0) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing netbase (6.5) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing readline-common (8.2-6) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31+nmu1) ... 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 libbrotli1:amd64 (1.1.0-2+b7) ... Removing libgnutls30t64:amd64 (3.8.9-3) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libffi8:amd64 (3.4.8-2) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libmbedcrypto16:amd64 (3.6.4-2) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-2) ... Processing triggers for libc-bin (2.41-12) ... 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'remove', '--allow-remove-essential', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libaec0:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-310:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libre2-11:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libtiff6: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', 'libxml2:amd64', 'libxrender1:amd64', 'media-types', 'ncbi-vdb-data', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-reportlab', 'python3-rlpycairo', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 0m54.9s INFO: Running scripts post_remove 0m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_remove_exceptions'] 0m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_remove_exceptions'] 0m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libaec0:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-310:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libre2-11:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libtiff6: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', 'libxml2:amd64', 'libxrender1:amd64', 'media-types', 'ncbi-vdb-data', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-reportlab', 'python3-rlpycairo', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 0m55.2s DUMP: dpkg: warning: ignoring request to remove bwa which isn't installed (Reading database ... 5002 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) ... Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libabsl20240722 which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed 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 libcom-err2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 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 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.84.3-1) ... 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 libgraphite2-3 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 libhdf5-310 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 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 libmagic-mgc which isn't installed Purging configuration files for libmagic1t64:amd64 (1:5.46-5) ... dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb3 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 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 (3.13.5-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libre2-11 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 libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 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 libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for media-types (13.0.0) ... Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... Purging configuration files for python3 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-minimal 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-pil 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 python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.5-2) ... 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+nmu1) ... Purging configuration files for sra-toolkit (3.2.1+dfsg-4) ... 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) ... 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libabsl20240722:amd64', 'libaec0:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-310:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libre2-11:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libtiff6: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', 'libxml2:amd64', 'libxrender1:amd64', 'media-types', 'ncbi-vdb-data', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-reportlab', 'python3-rlpycairo', 'python3.13', 'python3.13-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', 'seqsero'] 0m55.2s DUMP: dpkg: warning: ignoring request to remove seqsero which isn't installed 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', 'seqsero'] 0m55.2s INFO: Running scripts post_purge 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_purge_exceptions'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_purge_exceptions'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', '--pending'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--purge', '--pending'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--remove', '--pending'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg', '--remove', '--pending'] 0m55.2s INFO: Running scripts post_test 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_test_exceptions'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'tmp/scripts/post_test_exceptions'] 0m55.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m55.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-divert', '--list'] 0m55.4s 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 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'dpkg-divert', '--list'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'clean'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo', 'apt-get', 'clean'] 0m55.4s DEBUG: Recording chroot state 0m56.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/shm'] 0m56.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/shm'] 0m56.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/console'] 0m56.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/console'] 0m56.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/ptmx'] 0m56.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/ptmx'] 0m56.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/pts'] 0m56.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/dev/pts'] 0m56.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/proc'] 0m56.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo/proc'] 0m56.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m56.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3se8ggqo'] 0m56.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp3se8ggqo 0m56.2s INFO: PASS: Upgrading between Debian distributions. 0m56.2s INFO: PASS: All tests. 0m56.2s INFO: piuparts run ends. ret=0 End: 2025-08-12 12:59:50 GMT