Start: 2024-02-04 19:05:52 GMT [stable] Package: seqsero Version: 1.0.1+dfsg-4 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: all 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-4_all.deb Size: 357900 MD5sum: f7426f07494ac30aa54a6b196c617376 SHA256: 3f372ea7973cc9eb45151bdc61250fb34b4198fc171146e26e4cbe9f54ac144f [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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/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 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt seqsero=1.0.1+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp3onyaiuc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp3onyaiuc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/ptmx'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/ptmx'] 0m2.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/console'] 0m2.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/console'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/shm'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/shm'] 0m2.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp3onyaiuc/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'update'] 0m2.9s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'update'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s 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' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u2 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1+deb11u10 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m4.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 0m5.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 0m5.4s INFO: Running scripts is_testable 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/is_testable_uninstallable'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/is_testable_uninstallable'] 0m5.4s INFO: Running scripts pre_test 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_test_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_test_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_test_root_password'] 0m5.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_test_root_password'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m5.6s DUMP: Package: seqsero Version: 1.0.1+dfsg-4 Installed-Size: 3491 Maintainer: Debian Med Packaging Team Architecture: all 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-4_all.deb Size: 357900 MD5sum: f7426f07494ac30aa54a6b196c617376 SHA256: 3f372ea7973cc9eb45151bdc61250fb34b4198fc171146e26e4cbe9f54ac144f 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 0m5.6s INFO: apt-cache knows about the following packages: seqsero 0m5.6s INFO: Running scripts pre_install 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 0m5.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 0m5.8s DUMP: seqsero: Installed: (none) Candidate: 1.0.1+dfsg-4 Version table: 1.0.1+dfsg-4 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero'] 0m22.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bwa libaec0 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libfuse2 libgdbm-compat4 libgdbm6 libgfortran5 libhdf5-103-1 libhts3 libicu67 libimagequant0 libjbig0 libjpeg62-turbo libkdf5-2 liblapack3 liblcms2-2 libldap-2.4-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncurses6 libncursesw6 libnghttp2-14 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 mailcap media-types mime-support perl perl-modules-5.32 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-reportlab-accel python3.9 python3.9-minimal readline-common samtools sra-toolkit Suggested packages: fuse gdbm-l10n liblcms2-utils file libmbedtls-doc sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl 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-renderpm python3-psycopg2 python3-scipy raxml t-coffee wise w3-dtd-mathml gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pil-doc python3-pil-dbg python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool ispcr Recommended packages: ca-certificates libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-olefile python3-renderpm med-config The following NEW packages will be installed: bwa libaec0 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libfuse2 libgdbm-compat4 libgdbm6 libgfortran5 libhdf5-103-1 libhts3 libicu67 libimagequant0 libjbig0 libjpeg62-turbo libkdf5-2 liblapack3 liblcms2-2 libldap-2.4-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncurses6 libncursesw6 libnghttp2-14 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libtiff5 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 mailcap media-types mime-support perl perl-modules-5.32 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-reportlab-accel python3.9 python3.9-minimal readline-common samtools seqsero sra-toolkit 0 upgraded, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 47.1 MB of archives. After this operation, 197 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u2 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u2 [4106 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u2 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u9 [344 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libfuse2 amd64 2.9.9-5 [130 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get:43 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libmbedtls-dev amd64 2.16.9-0.1 [515 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libkdf5-2 amd64 2.10.9+dfsg-2 [20.8 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libncbi-vdb2 amd64 2.10.9+dfsg-2 [1266 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libncbi-wvdb2 amd64 2.10.9+dfsg-2 [1159 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1+deb11u2 [87.8 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1+deb11u2 [97.7 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab-accel amd64 3.5.59-2 [39.1 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 sra-toolkit amd64 2.10.9+dfsg-2 [5178 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 seqsero all 1.0.1+dfsg-4 [358 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.1 MB in 1s (35.4 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6666 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u2_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u2) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8931 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. 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Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../37-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libncbi-vdb2. Preparing to unpack .../38-libncbi-vdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-vdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package libncbi-wvdb2. Preparing to unpack .../39-libncbi-wvdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-wvdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../40-libncurses6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../41-libwebp6_0.6.1-2.1+deb11u2_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Selecting previously unselected package libtiff5:amd64. 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Preparing to unpack .../53-python3-biopython_1.78+dfsg-4_amd64.deb ... Unpacking python3-biopython (1.78+dfsg-4) ... Selecting previously unselected package samtools. Preparing to unpack .../54-samtools_1.11-1_amd64.deb ... Unpacking samtools (1.11-1) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../55-sra-toolkit_2.10.9+dfsg-2_amd64.deb ... Unpacking sra-toolkit (2.10.9+dfsg-2) ... Selecting previously unselected package seqsero. Preparing to unpack .../56-seqsero_1.0.1+dfsg-4_all.deb ... Unpacking seqsero (1.0.1+dfsg-4) ... Setting up media-types (4.0.0) ... Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up bwa (0.7.17-6+b1) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u2) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libfuse2:amd64 (2.9.9-5) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... 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 (1:2.0.6-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libwebpmux3:amd64 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... 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 (1.14-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1+deb11u2) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Setting up libmbedtls-dev:amd64 (2.16.9-0.1) ... Setting up libncbi-vdb2 (2.10.9+dfsg-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libncbi-wvdb2 (2.10.9+dfsg-2) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u2) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libkdf5-2 (2.10.9+dfsg-2) ... Setting up samtools (1.11-1) ... Setting up perl (5.32.1-4+deb11u2) ... Setting up mailcap (3.69) ... Setting up python3.9 (3.9.2-1) ... Setting up sra-toolkit (2.10.9+dfsg-2) ... Setting up mime-support (3.66) ... Setting up python3 (3.9.2-3) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-reportlab-accel:amd64 (3.5.59-2) ... Setting up python3-reportlab (3.5.59-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up seqsero (1.0.1+dfsg-4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero'] 0m22.8s INFO: Running scripts post_install 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 0m22.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 0m23.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 0m23.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3onyaiuc to sid 0m23.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m23.6s INFO: Running scripts pre_distupgrade 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'update'] 0m28.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9714 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7130 kB] Fetched 17.0 MB in 4s (4813 kB/s) Reading package lists... 0m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'update'] 0m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-yf', 'dist-upgrade'] 1m53.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libfuse2 libicu67 libkdf5-2 libldap-2.4-2 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-wvdb2 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libncbi-vdb2 libsemanage1 python3-reportlab-accel The following NEW packages will be installed: fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 gcc-14-base libcairo2 libcap2 libcurl4 libffi8 libfile-find-rule-perl libfontconfig1 libfontenc1 libfribidi0 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libhtscodecs2 libicu72 libldap-2.5-0 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncbi-vdb3 libncbi-wvdb3 libnumber-compare-perl libopenjp2-7 libperl5.38 libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libraqm0 libre2-10 libsemanage2 libsepol2 libsharpyuv0 libssl3 libtext-glob-perl libtiff6 libunistring5 libwebp7 libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxext6 libxrender1 ncbi-vdb-data netbase perl-modules-5.38 python3-cairo python3-chardet python3-freetype python3-rlpycairo python3.11 python3.11-minimal python3.12 python3.12-minimal sgml-base usrmerge w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils bwa coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-10-base gcc-9-base gpgv grep gzip hostname init-system-helpers libacl1 libaec0 libapt-pkg6.0 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libcurl3-gnutls libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libfreetype6 libfuse2 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libgmp10 libgnutls30 libgpg-error0 libgssapi-krb5-2 libhdf5-103-1 libhogweed6 libhts3 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblz4-1 liblzma5 libmagic-mgc libmagic1 libmbedtls-dev libmd0 libmount1 libmpdec3 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libpsl5 libpython3-stdlib libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libssh2-1 libstdc++6 libsystemd0 libsz2 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libwebpdemux2 libwebpmux3 libxcb1 libxml2 libxxhash0 libzstd1 login logsave lsb-base mailcap mawk media-types mount ncurses-base ncurses-bin passwd perl perl-base python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-reportlab readline-common samtools sed seqsero sra-toolkit sysvinit-utils tar tzdata util-linux zlib1g 147 upgraded, 69 newly installed, 3 to remove and 0 not upgraded. Need to get 120 MB of archives. After this operation, 241 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15 [2750 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240201-3 [42.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240201-3 [71.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.16 [88.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:8 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-6 [96.9 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] Get:11 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:12 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:14 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:15 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:16 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:17 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:18 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:19 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:20 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1 [140 kB] Get:21 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:22 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3+b1 [616 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:26 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:27 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:30 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2 [11.3 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-1 [16.9 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2 [48.4 kB] Get:36 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.85 [119 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1+b1 [65.8 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:41 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:42 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6 [159 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6 [190 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6 [117 kB] Get:48 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-6 [1230 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:50 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240201-3 [714 kB] Get:54 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-4+b2 [27.6 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-2 [362 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-2 [124 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.10 [982 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:69 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:71 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3+b1 [973 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1+b1 [50.1 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1+b1 [265 kB] Get:74 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:75 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:76 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:78 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.10 [1363 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:80 http://deb.debian.org/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:81 http://deb.debian.org/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:82 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:83 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:84 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:85 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-6 [32.1 kB] Get:86 http://deb.debian.org/debian sid/main amd64 lsb-base all 11.6 [4584 B] Get:87 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2+b2 [9140 B] Get:94 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libcurl4 amd64 8.6.0-1 [431 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.2-1 [23.4 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.2-1 [7684 B] Get:103 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1 amd64 1.10.10+repack-3 [1243 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:109 http://deb.debian.org/debian sid/main amd64 sra-toolkit amd64 3.0.3+dfsg-6 [6772 kB] Get:110 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libncbi-wvdb3 amd64 3.0.2+dfsg-2 [1078 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libre2-10 amd64 20230301-3 [187 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:119 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.0.9-1 [674 kB] Get:120 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.2.0-1 [525 kB] Get:121 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:122 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.81+dfsg-3 [1625 kB] Get:123 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:124 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:125 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240201-3 [136 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:131 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b2 [190 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-2 [1452 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1 [13.7 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:140 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4 [170 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.3 [107 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.3 [308 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.3 [107 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.3 [120 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:147 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:148 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:149 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:153 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-6 [29.7 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:158 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.1-2 [807 kB] Get:160 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.1-2 [2185 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:162 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-2 [148 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240201-3 [836 kB] Get:165 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-2 [2407 kB] Get:166 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:167 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:168 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:170 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:171 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:172 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1+b2 [23.3 kB] Get:174 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:175 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:176 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:177 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:178 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.2-6+b1 [316 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6+b1 [388 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:188 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.25.1-2 [140 kB] Get:189 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:190 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:191 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:192 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:194 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:195 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6 [143 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:201 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:202 http://deb.debian.org/debian sid/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240201-3 [147 kB] Get:204 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-2 [36.4 kB] Get:205 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.8-1 [125 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-1 [421 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libfuse2 amd64 2.9.9-8+b1 [119 kB] Get:209 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19-1 [644 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1 [92.8 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.18+ds-1 [441 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libmbedtls-dev amd64 2.28.7-1 [690 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:215 http://deb.debian.org/debian sid/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:216 http://deb.debian.org/debian sid/main amd64 seqsero amd64 1.0.1+dfsg-6 [358 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 120 MB in 1s (80.3 MB/s) (Reading database ... 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(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 ... 11674 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (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 ... 11672 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... 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Selecting previously unselected package libperl5.38:amd64. Preparing to unpack .../libperl5.38_5.38.2-3_amd64.deb ... Unpacking libperl5.38:amd64 (5.38.2-3) ... Preparing to unpack .../perl-base_5.38.2-3_amd64.deb ... Unpacking perl-base (5.38.2-3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.38.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13611 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5+b2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5+b2) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5+b2) ... (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 ... 13612 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2_all.deb ... Unpacking libaudit-common (1:3.1.2-2) over (1:3.0-2) ... Setting up libaudit-common (1:3.1.2-2) ... (Reading database ... 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Unpacking util-linux (2.39.3-6) over (2.36.1-8+deb11u1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux (2.39.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13610 files and directories currently installed.) 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(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 ... 13635 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (Reading database ... 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(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 ... 13647 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.4_all.deb ... Unpacking debian-archive-keyring (2023.4) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.4) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... 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(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 ... 13640 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... 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(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 ... 13654 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up perl (5.38.2-3) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 13669 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_39_all.deb ... Unpacking usrmerge (39) ... Setting up usrmerge (39) ... (Reading database ... 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(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 ... 13675 files and directories currently installed.) Preparing to unpack .../00-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b2) ... Preparing to unpack .../01-libgssapi-krb5-2_1.20.1-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-5) over (1.18.3-6+deb11u4) ... Preparing to unpack .../02-libkrb5-3_1.20.1-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-5) over (1.18.3-6+deb11u4) ... Preparing to unpack .../03-libk5crypto3_1.20.1-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-5) over (1.18.3-6+deb11u4) ... Preparing to unpack .../04-libkrb5support0_1.20.1-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-5) over (1.18.3-6+deb11u4) ... Preparing to unpack .../05-libcom-err2_1.47.0-2+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2+b1) over (1.46.2-2) ... Preparing to unpack .../06-libkeyutils1_1.6.3-2+b2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2+b2) over (1.6.1-2) ... Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) over (2.1.27+dfsg-2.1+deb11u1) ... Preparing to unpack .../08-libsasl2-2_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) over (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../09-libldap-2.5-0_2.5.13+dfsg-5+b3_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Preparing to unpack .../10-libnghttp2-14_1.59.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1) over (1.43.0-1) ... Preparing to unpack .../11-libpsl5_0.21.2-1+b1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1+b1) over (0.21.0-1.2) ... Preparing to unpack .../12-libssh2-1_1.11.0-4_amd64.deb ... Unpacking libssh2-1:amd64 (1.11.0-4) over (1.9.0-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../13-libcurl4_8.6.0-1_amd64.deb ... Unpacking libcurl4:amd64 (8.6.0-1) ... Preparing to unpack .../14-libaec0_1.1.2-1_amd64.deb ... Unpacking libaec0:amd64 (1.1.2-1) over (1.0.4-1) ... Preparing to unpack .../15-libsz2_1.1.2-1_amd64.deb ... Unpacking libsz2:amd64 (1.1.2-1) over (1.0.4-1) ... Preparing to unpack .../16-libhdf5-103-1_1.10.10+repack-3_amd64.deb ... Unpacking libhdf5-103-1:amd64 (1.10.10+repack-3) over (1.10.6+repack-4+deb11u1) ... Preparing to unpack .../17-libmagic1_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2+b1) over (1:5.39-3+deb11u1) ... Preparing to unpack .../18-libmagic-mgc_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) over (1:5.39-3+deb11u1) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../19-libmbedcrypto7_2.28.7-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.7-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../20-libmbedx509-1_2.28.7-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.7-1) ... Selecting previously unselected package libmbedtls14:amd64. Preparing to unpack .../21-libmbedtls14_2.28.7-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.7-1) ... Preparing to unpack .../22-sra-toolkit_3.0.3+dfsg-6_amd64.deb ... Unpacking sra-toolkit (3.0.3+dfsg-6) over (2.10.9+dfsg-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 ... 13747 files and directories currently installed.) Removing libncbi-vdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package ncbi-vdb-data. (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 ... 13695 files and directories currently installed.) Preparing to unpack .../0-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. Preparing to unpack .../1-libncbi-vdb3_3.0.2+dfsg-2_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Selecting previously unselected package libncbi-wvdb3:amd64. 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Preparing to unpack .../11-libmbedtls-dev_2.28.7-1_amd64.deb ... Unpacking libmbedtls-dev:amd64 (2.28.7-1) over (2.16.9-0.1) ... Preparing to unpack .../12-libmpdec3_2.5.1-2_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-2) over (2.5.1-1) ... Preparing to unpack .../13-libss2_1.47.0-2+b1_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2+b1) over (1.46.2-2) ... Preparing to unpack .../14-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) over (3.69) ... Preparing to unpack .../15-seqsero_1.0.1+dfsg-6_amd64.deb ... Unpacking seqsero (1.0.1+dfsg-6) over (1.0.1+dfsg-4) ... Setting up libhtscodecs2:amd64 (1.6.0-1) ... Setting up media-types (10.1.0) ... Installing new version of config file /etc/mime.types ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libsharpyuv0:amd64 (1.3.2-0.3) ... Setting up lsb-base (11.6) ... Setting up libkeyutils1:amd64 (1.6.3-2+b2) ... Setting up libpsl5:amd64 (0.21.2-1+b1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libicu72:amd64 (72.1-4) ... Setting up liblerc4:amd64 (4.0.0+ds-4) ... Setting up libre2-10:amd64 (20230301-3) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libglib2.0-0:amd64 (2.78.3-2) ... No schema files found: doing nothing. Setting up bwa (0.7.17-7+b3) ... Setting up libtirpc-common (1.3.4+ds-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.1-1) ... Setting up libpython3.12-minimal:amd64 (3.12.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.59.0-1) ... Setting up libmagic1:amd64 (1:5.45-2+b1) ... Setting up libdeflate0:amd64 (1.19-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libgomp1:amd64 (14-20240201-3) ... Setting up libfuse2:amd64 (2.9.9-8+b1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libaec0:amd64 (1.1.2-1) ... Setting up libkrb5support0:amd64 (1.20.1-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Feb 4 19:06:49 UTC 2024. Universal Time is now: Sun Feb 4 19:06:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up gcc-10-base:amd64 (10.5.0-2) ... Setting up libfontenc1:amd64 (1:1.1.4-1+b2) ... Setting up libblas3:amd64 (3.12.0-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libmbedcrypto7:amd64 (2.28.7-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libquadmath0:amd64 (14-20240201-3) ... Setting up libimagequant0:amd64 (2.18.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.42-1) ... Setting up libss2:amd64 (1.47.0-2+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5) ... Setting up logsave (1.47.0-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:amd64 (14-20240201-3) ... Setting up libwebp7:amd64 (1.3.2-0.3) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up mount (2.39.3-6) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b2) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libssh2-1:amd64 (1.11.0-4) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-5) ... Setting up libwebpmux3:amd64 (1.3.2-0.3) ... Setting up libbsd0:amd64 (0.11.8-1) ... Setting up mailcap (3.70+nmu1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up libsz2:amd64 (1.1.2-1) ... Setting up gcc-9-base:amd64 (9.5.0-5) ... Setting up python3.12-minimal (3.12.1-2) ... Setting up liblapack3:amd64 (3.12.0-2) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up fontconfig-config (2.14.2-6+b1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.3) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up e2fsprogs (1.47.0-2+b1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libmbedtls-dev:amd64 (2.28.7-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up libncbi-wvdb3:amd64 (3.0.2+dfsg-2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5) ... Setting up xml-core (0.19) ... Setting up libcurl4:amd64 (8.6.0-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libfontconfig1:amd64 (2.14.2-6+b1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libcurl3-gnutls:amd64 (8.6.0-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up libraqm0:amd64 (0.10.1-1) ... Setting up libhdf5-103-1:amd64 (1.10.10+repack-3) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up sra-toolkit (3.0.3+dfsg-6) ... Installing new version of config file /etc/ncbi/default.kfg ... Setting up libhts3:amd64 (1.18+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.1-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up samtools (1.19-1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.7-2) ... Setting up python3 (3.11.6-1) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-pil:amd64 (10.2.0-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-cairo (1.25.1-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.0.9-1) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for debianutils (5.16) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... Setting up seqsero (1.0.1+dfsg-6) ... 1m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-yf', 'dist-upgrade'] 1m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m54.7s DUMP: 927d67e88a5444ad4e9d652aa3f273fe - 1m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 1m55.0s 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 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'show', '--no-all-versions', 'seqsero'] 1m55.0s INFO: apt-cache knows about the following packages: seqsero 1m55.0s INFO: Running scripts pre_install 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 1m55.1s 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: 1m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 1m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 1m55.1s 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 1m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 1m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero'] 1m55.7s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-6). The following packages were automatically installed and are no longer required: libfuse2 libicu67 libkdf5-2 libldap-2.4-2 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-wvdb2 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero'] 1m55.7s INFO: Running scripts post_install 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 1m55.7s INFO: Running scripts post_distupgrade 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_exceptions'] 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_exceptions'] 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m55.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m55.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m55.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m55.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m55.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_distupgrade_zz_backports'] 1m55.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 1m57.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 1m57.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 1m58.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 1m58.4s INFO: Running scripts pre_install 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_database-server'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_exceptions'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_extras'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 1m58.4s 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: 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 1m58.5s 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 1m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-cache', 'policy', 'seqsero'] 1m58.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 1m59.0s DUMP: Reading package lists... Building dependency tree... Reading state information... seqsero is already the newest version (1.0.1+dfsg-6). The following packages were automatically installed and are no longer required: libfuse2 libicu67 libkdf5-2 libldap-2.4-2 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libmpdec3 libncbi-wvdb2 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m59.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', '-y', 'install', 'seqsero=1.0.1+dfsg-6'] 1m59.0s INFO: Running scripts post_install 1m59.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 1m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_install_exceptions'] 1m59.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m0.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m0.3s INFO: /bin converted to /usr/bin by /usr merge 2m0.4s INFO: /lib converted to /usr/lib by /usr merge 2m0.4s INFO: /lib/init converted to /usr/lib/init by /usr merge 2m0.4s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 2m0.4s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 2m0.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m0.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m0.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m0.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m0.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m0.4s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 2m0.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m0.4s INFO: /sbin converted to /usr/sbin by /usr merge 2m1.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', '-ac', '--ignore-obsolete'] 2m4.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', '-ac', '--ignore-obsolete'] 2m4.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m4.8s DUMP: 0.15.6 2m4.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m4.8s INFO: Running adequate version 0.15.6 now. 2m4.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'seqsero'] 2m5.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'seqsero'] 2m5.1s INFO: Running scripts pre_remove 2m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_exceptions'] 2m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/pre_remove_exceptions'] 2m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.10 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed bwa bwa 0.7.17-7+b3 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.85 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig-config fontconfig-config 2.14.2-6+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-3 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaec0:amd64 libaec0 1.1.2-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libblas3:amd64 libblas3 3.12.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.11.8-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-1 install ok installed libcurl4:amd64 libcurl4 8.6.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-2+b2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.2-6+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libfuse2:amd64 libfuse2 2.9.9-8+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5 install ok installed libgdbm6:amd64 libgdbm6 1.23-5 install ok installed libgfortran5:amd64 libgfortran5 14-20240201-3 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 14-20240201-3 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.10+repack-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.18+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkdf5-2 libkdf5-2 2.10.9+dfsg-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2+b2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblapack3:amd64 liblapack3 3.12.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmagic-mgc libmagic-mgc 1:5.45-2+b1 install ok installed libmagic1:amd64 libmagic1 1:5.45-2+b1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.28.7-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2 install ok installed libncbi-wvdb2 libncbi-wvdb2 2.10.9+dfsg-2 install ok installed libncbi-wvdb3:amd64 libncbi-wvdb3 3.0.2+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u2 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.42-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.7-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.7-2 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.1-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.1-2 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 14-20240201-3 install ok installed libraqm0:amd64 libraqm0 0.10.1-1 install ok installed libre2-10:amd64 libre2-10 20230301-3 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.3 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-3 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libsz2:amd64 libsz2 1.1.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u4 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255.3-2 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.3 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.3.2-0.3 install ok installed libwebpmux3:amd64 libwebpmux3 1.3.2-0.3 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed lsb-base lsb-base 11.6 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.39.3-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u2 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed python3 python3 3.11.6-1 install ok installed python3-biopython python3-biopython 1.81+dfsg-3 install ok installed python3-cairo python3-cairo 1.25.1-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-pil:amd64 python3-pil 10.2.0-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-reportlab python3-reportlab 4.0.9-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3.11 python3.11 3.11.7-2 install ok installed python3.11-minimal python3.11-minimal 3.11.7-2 install ok installed python3.12 python3.12 3.12.1-2 install ok installed python3.12-minimal python3.12-minimal 3.12.1-2 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.2-3 install ok installed samtools samtools 1.19-1 install ok installed sed sed 4.9-2 install ok installed seqsero seqsero 1.0.1+dfsg-6 install ok installed sgml-base sgml-base 1.31 install ok installed sra-toolkit sra-toolkit 3.0.3+dfsg-6 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-6 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 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 2m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'remove', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libkdf5-2', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb2', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libre2-10:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'netbase', 'perl-modules-5.32', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 2m52.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bwa fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libaec0 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libfuse2 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libicu67 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libkdf5-2 liblapack3 liblcms2-2 libldap-2.4-2 libldap-2.5-0 liblerc4 libmagic-mgc libmagic1 libmbedcrypto3 libmbedcrypto7 libmbedtls-dev libmbedtls12 libmbedtls14 libmbedx509-0 libmbedx509-1 libmpdec3 libncbi-vdb3 libncbi-wvdb2 libncbi-wvdb3 libncurses6 libncursesw6 libnghttp2-14 libopenjp2-7 libperl5.32 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libraqm0 libre2-10 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1 libsz2 libtiff5 libtiff6 libwebp6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 mailcap media-types mime-support ncbi-vdb-data netbase perl-modules-5.32 python3 python3-biopython python3-cairo python3-chardet python3-freetype python3-minimal python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-rlpycairo python3.11 python3.11-minimal python3.12 python3.12-minimal python3.9 python3.9-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, 127 to remove and 0 not upgraded. After this operation, 378 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 ... 16064 files and directories currently installed.) Removing seqsero (1.0.1+dfsg-6) ... Removing bwa (0.7.17-7+b3) ... Removing python3-biopython (1.81+dfsg-3) ... Removing python3-reportlab (4.0.9-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.25.1-2) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing libfontconfig1:amd64 (2.14.2-6+b1) ... Removing fontconfig-config (2.14.2-6+b1) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-7) ... Removing libkdf5-2 (2.10.9+dfsg-2) ... Removing sra-toolkit (3.0.3+dfsg-6) ... Removing libhdf5-103-1:amd64 (1.10.10+repack-3) ... Removing libsz2:amd64 (1.1.2-1) ... Removing libaec0:amd64 (1.1.2-1) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblapack3:amd64 (3.12.0-2) ... Removing libblas3:amd64 (3.12.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-pil:amd64 (10.2.0-1) ... Removing libraqm0:amd64 (0.10.1-1) ... Removing libcurl4:amd64 (8.6.0-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing samtools (1.19-1) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u4) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing libfontenc1:amd64 (1:1.1.4-1+b2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libfuse2:amd64 (2.9.9-8+b1) ... Removing libgfortran5:amd64 (14-20240201-3) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libglib2.0-0:amd64 (2.78.3-2) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgomp1:amd64 (14-20240201-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libhtscodecs2:amd64 (1.6.0-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libncbi-wvdb2 (2.10.9+dfsg-2) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4) ... Removing libmagic1:amd64 (1:5.45-2+b1) ... Removing libmagic-mgc (1:5.45-2+b1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libmbedtls-dev:amd64 (2.28.7-1) ... Removing libncbi-wvdb3:amd64 (3.0.2+dfsg-2) ... Removing libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b2) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u2) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libquadmath0:amd64 (14-20240201-3) ... Removing libre2-10:amd64 (20230301-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing libwebpmux3:amd64 (1.3.2-0.3) ... Removing libwebpdemux2:amd64 (1.3.2-0.3) ... Removing libwebp7:amd64 (1.3.2-0.3) ... Removing libsharpyuv0:amd64 (1.3.2-0.3) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing ncbi-vdb-data (3.0.2+dfsg-2) ... Removing perl-modules-5.32 (5.32.1-4+deb11u2) ... Removing python3-freetype (2.4.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.8-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing python3 (3.11.6-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing python3.11 (3.11.7-2) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.7-2) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Processing triggers for libc-bin (2.37-15) ... 2m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'remove', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libkdf5-2', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb2', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libre2-10:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'netbase', 'perl-modules-5.32', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'seqsero'] 2m52.8s INFO: Running scripts post_remove 2m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_remove_exceptions'] 2m52.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_remove_exceptions'] 2m52.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libkdf5-2', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb2', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libre2-10:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'netbase', 'perl-modules-5.32', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m53.2s DUMP: dpkg: warning: ignoring request to remove bwa which isn't installed (Reading database ... 7522 files and directories currently installed.) Purging configuration files for fontconfig-config (2.14.2-6+b1) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... dpkg: warning: ignoring request to remove fonts-dejavu-extra which isn't installed Purging configuration files for fonts-dejavu-mono (2.37-8) ... Purging configuration files for fonts-urw-base35 (20200910-7) ... 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 libcairo2 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 libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libfuse2 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.3-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed 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 libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libkdf5-2 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-2.4-2 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 (1:5.45-2+b1) ... dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed 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 libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb2 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb3 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 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 libpython3.11-minimal:amd64 (3.11.7-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.1-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-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 libre2-10 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 libsharpyuv0 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 libsz2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.1.0) ... 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 netbase (6.4) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed 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-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.7-2) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.1-2) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for sra-toolkit (3.0.3+dfsg-6) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed 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 (0.19) ... 2m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', 'bwa', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libaec0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libfuse2:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libkdf5-2', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb2', 'libncbi-wvdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libre2-10:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'mailcap', 'media-types', 'mime-support', 'ncbi-vdb-data', 'netbase', 'perl-modules-5.32', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-freetype', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-reportlab', 'python3-rlpycairo', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sgml-base', 'sra-toolkit', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 2m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', 'seqsero'] 2m53.2s DUMP: dpkg: warning: ignoring request to remove seqsero which isn't installed 2m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', 'seqsero'] 2m53.2s INFO: Running scripts post_purge 2m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_purge_exceptions'] 2m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_purge_exceptions'] 2m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', '--pending'] 2m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--purge', '--pending'] 2m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--remove', '--pending'] 2m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg', '--remove', '--pending'] 2m53.3s INFO: Running scripts post_test 2m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_test_exceptions'] 2m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'tmp/scripts/post_test_exceptions'] 2m53.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m53.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-divert', '--list'] 2m53.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 2m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'dpkg-divert', '--list'] 2m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'clean'] 2m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc', 'apt-get', 'clean'] 2m53.9s DEBUG: Recording chroot state 2m55.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/shm'] 2m55.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/shm'] 2m55.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/console'] 2m55.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/console'] 2m55.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/ptmx'] 2m55.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/ptmx'] 2m55.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts'] 2m55.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/dev/pts'] 2m55.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/proc'] 2m55.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc/proc'] 2m55.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m55.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3onyaiuc'] 2m55.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp3onyaiuc 2m55.6s INFO: PASS: Upgrading between Debian distributions. 2m55.6s INFO: PASS: All tests. 2m55.6s INFO: piuparts run ends. ret=0 End: 2024-02-04 19:08:48 GMT