Start: 2022-10-01 03:52:32 GMT [testing] 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 [sid] 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/sbin/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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpimg7e2c_ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpimg7e2c_ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/proc'] 0m2.8s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/proc'] 0m2.8s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts'] 0m2.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts'] 0m2.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/ptmx'] 0m2.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/ptmx'] 0m2.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/console'] 0m2.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/console'] 0m2.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/shm'] 0m2.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/shm'] 0m2.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.8s DEBUG: Created policy-rc.d and chmodded it. 0m2.8s DEBUG: Created resolv.conf. 0m2.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpimg7e2c_/tmp/scripts/ 0m2.8s INFO: Running scripts post_chroot_unpack 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'update'] 0m6.4s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [161 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8568 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5806 kB] Fetched 14.5 MB in 3s (5446 kB/s) Reading package lists... 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'update'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-yf', 'dist-upgrade'] 0m9.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: coreutils libc-bin libc6 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6660 kB of archives. After this operation, 15.4 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.35-1 [2941 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.35-1 [822 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6660 kB in 0s (52.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8606 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1_amd64.deb ... Unpacking coreutils (9.1-1) over (8.32-4.1+b1) ... Setting up coreutils (9.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8605 files and directories currently installed.) Preparing to unpack .../libc6_2.35-1_amd64.deb ... Unpacking libc6:amd64 (2.35-1) over (2.34-8) ... Setting up libc6:amd64 (2.35-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8604 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-1_amd64.deb ... Unpacking libc-bin (2.35-1) over (2.34-8) ... Setting up libc-bin (2.35-1) ... 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-yf', 'dist-upgrade'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s DUMP: e041a35f1801e8f3f04f0f3d69053875 - 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s INFO: Running scripts post_setup 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_dummy_users'] 0m10.8s DUMP: useradd warning: dummy100's uid 100 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_dummy_users'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_forbid_home'] 0m10.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_forbid_home'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_minimize'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_minimize'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_zz_backports'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_setup_zz_backports'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.9s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.2 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2~rc2-2 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.2 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022c-1 install ok installed usr-is-merged usr-is-merged 31 install ok installed usrmerge usrmerge 31 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m11.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 0m11.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 0m11.6s INFO: Running scripts is_testable 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/is_testable_uninstallable'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/is_testable_uninstallable'] 0m11.6s INFO: Running scripts pre_test 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_test_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_test_exceptions'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_test_root_password'] 0m11.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_test_root_password'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m11.9s 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 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m11.9s INFO: apt-cache knows about the following packages: seqsero 0m11.9s INFO: Running scripts pre_install 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 0m12.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 0m12.1s DUMP: seqsero: Installed: (none) Candidate: 1.0.1+dfsg-6 Version table: 1.0.1+dfsg-6 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero'] 1m15.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bwa fonts-urw-base35 libaec0 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libfuse2 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libicu71 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmd0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 mailcap media-types mime-support ncbi-vdb-data python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.10 python3.10-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 fuse krb5-doc krb5-user liblcms2-utils file libmbedtls-doc python3-doc python3-tk python3-venv clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.10-venv python3.10-doc binutils binfmt-support readline-doc cwltool ispcr sgml-base-doc debhelper Recommended packages: ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils python-biopython-doc ncbi-blast+ python3-olefile med-config The following NEW packages will be installed: bwa fonts-urw-base35 libaec0 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libfuse2 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libicu71 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmd0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 mailcap media-types mime-support ncbi-vdb-data python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.10 python3.10-minimal readline-common samtools seqsero sgml-base sra-toolkit w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 56.8 MB of archives. After this operation, 196 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.5-2 [2030 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-minimal amd64 3.10.7-1 [828 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.4.9-1 [105 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.10-minimal amd64 3.10.7-1 [1994 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.10.6-1 [38.7 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 8.0.0 [33.4 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20-1 [65.7 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20-1 [111 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20-1 [363 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20-1 [166 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2~rc2-2 [75.8 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2~rc2-2 [173 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.39.3-1 [844 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libpython3.10-stdlib amd64 3.10.7-1 [1685 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 python3.10 amd64 3.10.7-1 [547 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.10.6-1 [21.7 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.10.6-1 [38.2 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.30 [15.1 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 bwa amd64 0.7.17-7 [212 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b4 [275 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.38-2 [290 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-3 [420 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.1 [573 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-4 [6375 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.10.1-2 [156 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.6-1 [114 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-8 [38.7 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-8 [78.2 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-1 [230 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.50.0-1 [76.1 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libglib2.0-0 amd64 2.74.0-1 [1463 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-3 [116 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 5.2.0-2 [1890 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:59 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack-1 [1254 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.2.2-1 [54.1 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.13+ds-2+b1 [397 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libicu71 amd64 71.1-3 [9218 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.2-1+b1 [169 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.1-1 [274 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.1-1 [129 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.1-1 [164 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libmbedtls-dev amd64 2.28.1-1 [678 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libkdf5-2 amd64 2.11.2+dfsg-6 [24.6 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.10.1-2 [2202 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.13.1-1+b1 [153 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-1 [170 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1+b1 [708 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 2.11.2+dfsg-6 [73.2 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb2 amd64 2.11.2+dfsg-6 [1226 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libncbi-wvdb2 amd64 2.11.2+dfsg-6 [1174 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1 [189 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4 [11.0 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.2-2+b1 [277 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libtiff5 amd64 4.4.0-4 [314 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.2-2+b1 [98.4 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.2-2+b1 [108 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 59.6.0-1.2 [196 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.21.5-1+b1 [3227 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.11-1 [82.4 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.11-1 [42.3 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.2.0-1+b1 [467 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.11-1 [566 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.79+dfsg-3+b1 [1425 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.13-4+b1 [577 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 sra-toolkit amd64 2.11.3+dfsg-1+b1 [5130 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 seqsero amd64 1.0.1+dfsg-6 [358 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.8 MB in 5s (10.5 MB/s) Selecting previously unselected package libssl3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8605 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.5-2_amd64.deb ... Unpacking libssl3:amd64 (3.0.5-2) ... Selecting previously unselected package libpython3.10-minimal:amd64. Preparing to unpack .../libpython3.10-minimal_3.10.7-1_amd64.deb ... Unpacking libpython3.10-minimal:amd64 (3.10.7-1) ... Selecting previously unselected package libexpat1:amd64. 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Setting up libblas3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.2-1+b1) ... Setting up libmbedcrypto7:amd64 (2.28.1-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.3+20220423-2) ... Setting up xfonts-encodings (1:1.0.4-2.1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-3) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libpng16-16:amd64 (1.6.38-2) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libk5crypto3:amd64 (1.20-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-8) ... Setting up libgfortran5:amd64 (12.2.0-3) ... Setting up libwebp7:amd64 (1.2.2-2+b1) ... Setting up libmd0:amd64 (1.0.4-2) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libopenjp2-7:amd64 (2.5.0-1) ... Setting up ncbi-vdb-data (2.11.2+dfsg-6) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.30) ... Setting up libkrb5-3:amd64 (1.20-1) ... Setting up libtiff5:amd64 (4.4.0-4) ... Setting up libwebpmux3:amd64 (1.2.2-2+b1) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up mailcap (3.70+nmu1) ... Setting up readline-common (8.2~rc2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1+b1) ... Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up mime-support (3.66) ... Setting up libmbedx509-1:amd64 (2.28.1-1) ... Setting up libmbedtls14:amd64 (2.28.1-1) ... Setting up libwebpdemux2:amd64 (1.2.2-2+b1) ... Setting up libreadline8:amd64 (8.2~rc2-2) ... Setting up libmbedtls-dev:amd64 (2.28.1-1) ... Setting up libncbi-vdb2:amd64 (2.11.2+dfsg-6) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-3) ... Setting up libncbi-wvdb2:amd64 (2.11.2+dfsg-6) ... Setting up libgssapi-krb5-2:amd64 (1.20-1) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:amd64 (7.85.0-1) ... Setting up libharfbuzz0b:amd64 (5.2.0-2) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libcurl3-gnutls:amd64 (7.85.0-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libraqm0:amd64 (0.7.0-4) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libhts3:amd64 (1.13+ds-2+b1) ... Setting up fonts-urw-base35 (20200910-4) ... Setting up libkdf5-2:amd64 (2.11.2+dfsg-6) ... Setting up samtools (1.13-4+b1) ... Setting up libpython3.10-stdlib:amd64 (3.10.7-1) ... Setting up libpython3-stdlib:amd64 (3.10.6-1) ... Setting up sra-toolkit (2.11.3+dfsg-1+b1) ... Setting up python3.10 (3.10.7-1) ... Setting up python3 (3.10.6-1) ... Setting up python3-pil:amd64 (9.2.0-1+b1) ... Setting up python3-reportlab-accel:amd64 (3.6.11-1) ... Setting up python3-reportlab (3.6.11-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-renderpm:amd64 (3.6.11-1) ... Setting up python3-numpy (1:1.21.5-1+b1) ... Processing triggers for libc-bin (2.35-1) ... Processing triggers for sgml-base (1.30) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.79+dfsg-3+b1) ... Setting up seqsero (1.0.1+dfsg-6) ... 1m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero'] 1m15.2s INFO: Running scripts post_install 1m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m15.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m16.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m16.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpimg7e2c_ to sid 1m16.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m16.0s INFO: Running scripts pre_distupgrade 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_exceptions'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_exceptions'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'update'] 1m20.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [158 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9350 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6911 kB] Fetched 16.4 MB in 3s (4928 kB/s) Reading package lists... 1m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'update'] 1m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-yf', 'dist-upgrade'] 1m24.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bash grep libapt-pkg6.0 libffi8 libglib2.0-0 libhts3 libhtscodecs2 libldap-2.5-0 libreadline8 libssl3 python3-pkg-resources readline-common samtools tzdata usr-is-merged usrmerge 17 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 10.2 MB of archives. After this operation, 777 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2-1 [1524 kB] Get:2 http://deb.debian.org/debian sid/main amd64 grep amd64 3.8-2 [432 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.5.3 [1044 kB] Get:4 http://deb.debian.org/debian sid/main amd64 apt amd64 2.5.3 [1505 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.3-2 [26.1 kB] Get:6 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 32 [5524 B] Get:7 http://deb.debian.org/debian sid/main amd64 usrmerge all 32 [13.2 kB] Get:8 http://deb.debian.org/debian sid/main amd64 tzdata all 2022d-1 [290 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-1 [76.0 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.74.0-2 [1463 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.3.0-2 [87.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.5-4 [2031 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.16+ds-1 [433 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-2 [230 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-1 [173 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 65.3.0-1.1 [281 kB] Get:17 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.16.1-1 [607 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.2 MB in 0s (42.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12861 files and directories currently installed.) Preparing to unpack .../archives/bash_5.2-1_amd64.deb ... Unpacking bash (5.2-1) over (5.2~rc2-2) ... Setting up bash (5.2-1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12861 files and directories currently installed.) Preparing to unpack .../archives/grep_3.8-2_amd64.deb ... Unpacking grep (3.8-2) over (3.7-1) ... Setting up grep (3.8-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12863 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.5.3_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.5.3) over (2.5.2) ... Setting up libapt-pkg6.0:amd64 (2.5.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12863 files and directories currently installed.) Preparing to unpack .../archives/apt_2.5.3_amd64.deb ... Unpacking apt (2.5.3) over (2.5.2) ... Setting up apt (2.5.3) ... adduser: The user `_apt' already exists, but is not a system user. Exiting. (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 ... 12863 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.3-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.3-2) over (3.4.2-4) ... Setting up libffi8:amd64 (3.4.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12863 files and directories currently installed.) Preparing to unpack .../usr-is-merged_32_all.deb ... W: /etc/unsupported-skip-usrmerge-conversion exists. Unpacking usr-is-merged (32) over (31) ... Setting up usr-is-merged (32) ... (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 ... 12863 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_32_all.deb ... Unpacking usrmerge (32) over (31) ... Setting up usrmerge (32) ... W: /etc/unsupported-skip-usrmerge-conversion exists. (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 ... 12863 files and directories currently installed.) Preparing to unpack .../0-tzdata_2022d-1_all.deb ... Unpacking tzdata (2022d-1) over (2022c-1) ... Preparing to unpack .../1-readline-common_8.2-1_all.deb ... Unpacking readline-common (8.2-1) over (8.2~rc2-2) ... Preparing to unpack .../2-libglib2.0-0_2.74.0-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.0-2) over (2.74.0-1) ... Preparing to unpack .../3-libhtscodecs2_1.3.0-2_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-2) over (1.2.2-1) ... Preparing to unpack .../4-libssl3_3.0.5-4_amd64.deb ... Unpacking libssl3:amd64 (3.0.5-4) over (3.0.5-2) ... Preparing to unpack .../5-libhts3_1.16+ds-1_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-1) over (1.13+ds-2+b1) ... Preparing to unpack .../6-libldap-2.5-0_2.5.13+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-2) over (2.5.13+dfsg-1) ... Preparing to unpack .../7-libreadline8_8.2-1_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1) over (8.2~rc2-2) ... Preparing to unpack .../8-python3-pkg-resources_65.3.0-1.1_all.deb ... Unpacking python3-pkg-resources (65.3.0-1.1) over (59.6.0-1.2) ... Preparing to unpack .../9-samtools_1.16.1-1_amd64.deb ... Unpacking samtools (1.16.1-1) over (1.13-4+b1) ... Setting up python3-pkg-resources (65.3.0-1.1) ... Setting up libhtscodecs2:amd64 (1.3.0-2) ... Setting up libglib2.0-0:amd64 (2.74.0-2) ... No schema files found: doing nothing. Setting up libssl3:amd64 (3.0.5-4) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-2) ... Setting up tzdata (2022d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 1 03:53:56 UTC 2022. Universal Time is now: Sat Oct 1 03:53:56 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up readline-common (8.2-1) ... Setting up libhts3:amd64 (1.16+ds-1) ... Setting up libreadline8:amd64 (8.2-1) ... Setting up samtools (1.16.1-1) ... Processing triggers for libc-bin (2.35-1) ... Processing triggers for debianutils (5.7-0.3) ... 1m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-yf', 'dist-upgrade'] 1m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m25.5s DUMP: 543b449026dd0f1cc204f79d1a550fae - 1m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 1m25.9s 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 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 1m25.9s INFO: apt-cache knows about the following packages: seqsero 1m25.9s INFO: Running scripts pre_install 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 1m26.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 1m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 1m26.0s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 1m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 1m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero'] 1m26.6s 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. 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero'] 1m26.6s INFO: Running scripts post_install 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m26.6s INFO: Running scripts post_distupgrade 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_exceptions'] 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_exceptions'] 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_zz_backports'] 1m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_distupgrade_zz_backports'] 1m26.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m27.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m27.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m27.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m27.7s INFO: Running scripts pre_install 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_database-server'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_exceptions'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_extras'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m27.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m27.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 1m27.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy'] 1m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 1m27.9s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 1m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-cache', 'policy', 'seqsero'] 1m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 1m28.5s 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. 1m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 1m28.5s INFO: Running scripts post_install 1m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_install_exceptions'] 1m28.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m29.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 1m29.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', '-ac', '--ignore-obsolete'] 1m31.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', '-ac', '--ignore-obsolete'] 1m31.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m31.1s DUMP: 0.15.6 1m31.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m31.1s INFO: Running adequate version 0.15.6 now. 1m31.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'seqsero'] 1m31.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'seqsero'] 1m31.2s INFO: Running scripts pre_remove 1m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m33.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m33.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m33.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m33.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_exceptions'] 1m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/pre_remove_exceptions'] 1m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m33.6s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-1 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed bwa bwa 0.7.17-7 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.8-2 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libaec0:amd64 libaec0 1.0.6-1+b1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1 install ok installed libblas3:amd64 libblas3 3.10.1-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b4 install ok installed libbsd0:amd64 libbsd0 0.11.6-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.85.0-1 install ok installed libcurl4:amd64 libcurl4 7.85.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libdeflate0:amd64 libdeflate0 1.12-1 install ok installed libexpat1:amd64 libexpat1 2.4.9-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.3-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libfuse2:amd64 libfuse2 2.9.9-5 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-3 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgomp1:amd64 libgomp1 12.2.0-3 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20-1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 5.2.0-2 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.8+repack-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-2 install ok installed libicu71:amd64 libicu71 71.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.2-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20-1 install ok installed libkdf5-2:amd64 libkdf5-2 2.11.2+dfsg-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-1 install ok installed libkrb5-3:amd64 libkrb5-3 1.20-1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20-1 install ok installed liblapack3:amd64 liblapack3 3.10.1-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.13.1-1+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmagic-mgc libmagic-mgc 1:5.41-4 install ok installed libmagic1:amd64 libmagic1 1:5.41-4 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.1-1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.28.1-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.1-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.1-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncbi-vdb2:amd64 libncbi-vdb2 2.11.2+dfsg-6 install ok installed libncbi-wvdb2:amd64 libncbi-wvdb2 2.11.2+dfsg-6 install ok installed libncurses6:amd64 libncurses6 6.3+20220423-2 install ok installed libncursesw6:amd64 libncursesw6 6.3+20220423-2 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.50.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libpng16-16:amd64 libpng16-16 1.6.38-2 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.10.6-1 install ok installed libpython3.10-minimal:amd64 libpython3.10-minimal 3.10.7-1 install ok installed libpython3.10-stdlib:amd64 libpython3.10-stdlib 3.10.7-1 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-3 install ok installed libraqm0:amd64 libraqm0 0.7.0-4 install ok installed libreadline8:amd64 libreadline8 8.2-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.39.3-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.5-4 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libsz2:amd64 libsz2 1.0.6-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtiff5:amd64 libtiff5 4.4.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libwebp7:amd64 libwebp7 1.2.2-2+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.2-2+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.2-2+b1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 8.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.38.1-1 install ok installed ncbi-vdb-data ncbi-vdb-data 2.11.2+dfsg-6 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed python3 python3 3.10.6-1 install ok installed python3-biopython python3-biopython 1.79+dfsg-3+b1 install ok installed python3-minimal python3-minimal 3.10.6-1 install ok installed python3-numpy python3-numpy 1:1.21.5-1+b1 install ok installed python3-pil:amd64 python3-pil 9.2.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 65.3.0-1.1 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.11-1 install ok installed python3-reportlab python3-reportlab 3.6.11-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.11-1 install ok installed python3.10 python3.10 3.10.7-1 install ok installed python3.10-minimal python3.10-minimal 3.10.7-1 install ok installed readline-common readline-common 8.2-1 install ok installed samtools samtools 1.16.1-1 install ok installed sed sed 4.8-1 install ok installed seqsero seqsero 1.0.1+dfsg-6 install ok installed sgml-base sgml-base 1.30 install ok installed sra-toolkit sra-toolkit 2.11.3+dfsg-1+b1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022d-1 install ok installed usr-is-merged usr-is-merged 32 install ok installed usrmerge usrmerge 32 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.1 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 1m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'remove', 'bwa', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu71:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2:amd64', 'libncbi-wvdb2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxml2:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.10', 'python3.10-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 2m18.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bwa fonts-urw-base35 libaec0 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libfuse2 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libicu71 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkdf5-2 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmd0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libpng16-16 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtiff5 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 mailcap media-types mime-support ncbi-vdb-data python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.10 python3.10-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, 101 to remove and 0 not upgraded. After this operation, 197 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 ... 12894 files and directories currently installed.) Removing seqsero (1.0.1+dfsg-6) ... Removing bwa (0.7.17-7) ... Removing python3-biopython (1.79+dfsg-3+b1) ... Removing python3-renderpm:amd64 (3.6.11-1) ... Removing fonts-urw-base35 (20200910-4) ... Removing sra-toolkit (2.11.3+dfsg-1+b1) ... Removing libkdf5-2:amd64 (2.11.2+dfsg-6) ... Removing libhdf5-103-1:amd64 (1.10.8+repack-1) ... Removing libsz2:amd64 (1.0.6-1+b1) ... Removing libaec0:amd64 (1.0.6-1+b1) ... Removing python3-numpy (1:1.21.5-1+b1) ... Removing liblapack3:amd64 (3.10.1-2) ... Removing libblas3:amd64 (3.10.1-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-reportlab (3.6.11-1) ... Removing python3-pil:amd64 (9.2.0-1+b1) ... Removing libraqm0:amd64 (0.7.0-4) ... Removing libcurl4:amd64 (7.85.0-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.6-1) ... Removing samtools (1.16.1-1) ... Removing libhts3:amd64 (1.16+ds-1) ... Removing libcurl3-gnutls:amd64 (7.85.0-1) ... Removing libtiff5:amd64 (4.4.0-4) ... Removing libdeflate0:amd64 (1.12-1) ... Removing python3-reportlab-accel:amd64 (3.6.11-1) ... Removing python3-pkg-resources (65.3.0-1.1) ... Removing python3 (3.10.6-1) ... Removing python3.10 (3.10.7-1) ... Removing python3-minimal (3.10.6-1) ... Removing python3.10-minimal (3.10.7-1) ... Removing libexpat1:amd64 (2.4.9-1) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libfuse2:amd64 (2.9.9-5) ... Removing libgfortran5:amd64 (12.2.0-3) ... Removing libharfbuzz0b:amd64 (5.2.0-2) ... Removing libglib2.0-0:amd64 (2.74.0-2) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgomp1:amd64 (12.2.0-3) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libpython3-stdlib:amd64 (3.10.6-1) ... Removing libpython3.10-stdlib:amd64 (3.10.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20-1) ... Removing libhtscodecs2:amd64 (1.3.0-2) ... Removing libncbi-wvdb2:amd64 (2.11.2+dfsg-6) ... Removing libncbi-vdb2:amd64 (2.11.2+dfsg-6) ... Removing libxml2:amd64 (2.9.14+dfsg-1+b1) ... Removing libicu71:amd64 (71.1-3) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.2-1+b1) ... Removing libkrb5-3:amd64 (1.20-1) ... Removing libk5crypto3:amd64 (1.20-1) ... Removing libkeyutils1:amd64 (1.6.3-1) ... Removing libkrb5support0:amd64 (1.20-1) ... Removing liblcms2-2:amd64 (2.13.1-1+b1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-1) ... Removing libmagic1:amd64 (1:5.41-4) ... Removing libmagic-mgc (1:5.41-4) ... Removing libmbedtls-dev:amd64 (2.28.1-1) ... Removing libmbedtls14:amd64 (2.28.1-1) ... Removing libmbedx509-1:amd64 (2.28.1-1) ... Removing libmbedcrypto7:amd64 (2.28.1-1) ... Removing libmd0:amd64 (1.0.4-2) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncurses6:amd64 (6.3+20220423-2) ... Removing libncursesw6:amd64 (6.3+20220423-2) ... Removing libnghttp2-14:amd64 (1.50.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-1) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libpython3.10-minimal:amd64 (3.10.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-3) ... Removing libreadline8:amd64 (8.2-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-8) ... Removing libsqlite3-0:amd64 (3.39.3-1) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing libssl3:amd64 (3.0.5-4) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebpmux3:amd64 (1.2.2-2+b1) ... Removing libwebpdemux2:amd64 (1.2.2-2+b1) ... Removing libwebp7:amd64 (1.2.2-2+b1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing media-types (8.0.0) ... Removing ncbi-vdb-data (2.11.2+dfsg-6) ... Removing readline-common (8.2-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.30) ... Removing xfonts-encodings (1:1.0.4-2.1) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.12.1+dfsg-3) ... Removing libbrotli1:amd64 (1.0.9-2+b4) ... Removing libpng16-16:amd64 (1.6.38-2) ... Processing triggers for libc-bin (2.35-1) ... 2m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'remove', 'bwa', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu71:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2:amd64', 'libncbi-wvdb2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxml2:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.10', 'python3.10-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 2m18.1s INFO: Running scripts post_remove 2m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_remove_exceptions'] 2m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_remove_exceptions'] 2m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', 'bwa', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu71:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2:amd64', 'libncbi-wvdb2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxml2:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.10', 'python3.10-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m18.4s DUMP: dpkg: warning: ignoring request to remove bwa which isn't installed (Reading database ... 8651 files and directories currently installed.) Purging configuration files for fonts-urw-base35 (20200910-4) ... dpkg: warning: ignoring request to remove libaec0 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 libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 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 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 libfuse2 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.0-2) ... 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 (1.20-1) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libicu71 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 libkdf5-2 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 libldap-2.5-0 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 libmagic1:amd64 (1:5.41-4) ... dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls-dev which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmd0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb2 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb2 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 libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.10-minimal:amd64 (3.10.7-1) ... dpkg: warning: ignoring request to remove libpython3.10-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 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 libxau6 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 libxml2 which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (8.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed Purging configuration files for python3 (3.10.6-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3.10 which isn't installed Purging configuration files for python3.10-minimal (3.10.7-1) ... Purging configuration files for readline-common (8.2-1) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.30) ... Purging configuration files for sra-toolkit (2.11.3+dfsg-1+b1) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', 'bwa', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu71:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkdf5-2:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncbi-vdb2:amd64', 'libncbi-wvdb2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxml2:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.10', 'python3.10-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', 'seqsero'] 2m18.4s DUMP: dpkg: warning: ignoring request to remove seqsero which isn't installed 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', 'seqsero'] 2m18.4s INFO: Running scripts post_purge 2m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_purge_exceptions'] 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_purge_exceptions'] 2m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', '--pending'] 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--purge', '--pending'] 2m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--remove', '--pending'] 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg', '--remove', '--pending'] 2m18.4s INFO: Running scripts post_test 2m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_test_exceptions'] 2m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'tmp/scripts/post_test_exceptions'] 2m18.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 2m18.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 2m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-divert', '--list'] 2m18.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 2m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'dpkg-divert', '--list'] 2m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'clean'] 2m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_', 'apt-get', 'clean'] 2m18.9s DEBUG: Recording chroot state 2m20.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/shm'] 2m20.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/shm'] 2m20.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/console'] 2m20.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/console'] 2m20.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/ptmx'] 2m20.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/ptmx'] 2m20.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts'] 2m20.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/dev/pts'] 2m20.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/proc'] 2m20.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_/proc'] 2m20.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 2m20.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpimg7e2c_'] 2m20.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpimg7e2c_ 2m20.3s INFO: PASS: Upgrading between Debian distributions. 2m20.3s INFO: PASS: All tests. 2m20.3s INFO: piuparts run ends. ret=0 End: 2022-10-01 03:54:52 GMT