Start: 2024-01-13 05:19:58 GMT [bullseye] Package: seer Version: 1.1.4-5 Installed-Size: 4834 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), libtext-csv-perl Suggests: fsm-lite Description: genomic sequence element (kmer) enrichment analysis Homepage: https://github.com/johnlees/seer Description-md5: 979255ced90d884824e6cb3db05419ed Section: science Priority: optional Filename: pool/main/s/seer/seer_1.1.4-5_amd64.deb Size: 1176264 MD5sum: 96e6e00be7b9fc6acdbd48002f981451 SHA256: a23129eafa63f6a94ba827b4d801ee79ff1ab0983ca2b9f785c8c0b24bf3c242 [bullseye-next] Package: seer Version: 1.1.4-5 Installed-Size: 4834 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), libtext-csv-perl Suggests: fsm-lite Description: genomic sequence element (kmer) enrichment analysis Homepage: https://github.com/johnlees/seer Description-md5: 979255ced90d884824e6cb3db05419ed Section: science Priority: optional Filename: pool/main/s/seer/seer_1.1.4-5_amd64.deb Size: 1176264 MD5sum: 96e6e00be7b9fc6acdbd48002f981451 SHA256: a23129eafa63f6a94ba827b4d801ee79ff1ab0983ca2b9f785c8c0b24bf3c242 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 --warn-on-usr-move fail --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 bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt seer=1.1.4-5 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 1.2 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 --warn-on-usr-move fail --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 bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt seer=1.1.4-5 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/tmpp1qsn703 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpp1qsn703 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/proc'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/proc'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/ptmx'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/ptmx'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/console'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/console'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpp1qsn703/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'update'] 0m2.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s INFO: Running scripts post_setup 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s 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' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.4s 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 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m4.8s INFO: Running scripts is_testable 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s INFO: Running scripts pre_test 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'show', '--no-all-versions', 'seer'] 0m5.1s DUMP: Package: seer Version: 1.1.4-5 Installed-Size: 4834 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), libtext-csv-perl Suggests: fsm-lite Description-en: genomic sequence element (kmer) enrichment analysis Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics. Description-md5: 979255ced90d884824e6cb3db05419ed Homepage: https://github.com/johnlees/seer Section: science Priority: optional Filename: pool/main/s/seer/seer_1.1.4-5_amd64.deb Size: 1176264 MD5sum: 96e6e00be7b9fc6acdbd48002f981451 SHA256: a23129eafa63f6a94ba827b4d801ee79ff1ab0983ca2b9f785c8c0b24bf3c242 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'show', '--no-all-versions', 'seer'] 0m5.1s INFO: apt-cache knows about the following packages: seer 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m5.1s 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: 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m5.2s DUMP: seer: Installed: (none) Candidate: 1.1.4-5 Version table: 1.1.4-5 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer'] 0m7.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libaec0 libarmadillo10 libarpack2 libblas3 libboost-program-options1.74.0 libgdbm-compat4 libgdbm6 libgfortran5 libgzstream0 libhdf5-103-1 liblapack3 libperl5.32 libquadmath0 libsuperlu5 libsz2 libtext-csv-perl perl perl-modules-5.32 Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl fsm-lite Recommended packages: libtext-csv-xs-perl netbase The following NEW packages will be installed: libaec0 libarmadillo10 libarpack2 libblas3 libboost-program-options1.74.0 libgdbm-compat4 libgdbm6 libgfortran5 libgzstream0 libhdf5-103-1 liblapack3 libperl5.32 libquadmath0 libsuperlu5 libsz2 libtext-csv-perl perl perl-modules-5.32 seer 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 13.7 MB of archives. After this operation, 71.3 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 libaec0 amd64 1.0.4-1 [20.3 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libarpack2 amd64 3.8.0-1 [103 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libsuperlu5 amd64 5.2.2+dfsg1-2 [163 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libarmadillo10 amd64 1:10.1.2+dfsg-6+b1 [98.8 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libgzstream0 amd64 1.5+dfsg-5 [6712 B] Get:16 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get:17 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libtext-csv-perl all 2.00-1 [105 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 seer amd64 1.1.4-5 [1176 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.7 MB in 0s (56.9 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 .../00-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 .../01-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../02-libgdbm-compat4_1.19-2_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.19-2) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../03-libperl5.32_5.32.1-4+deb11u2_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u2) ... Selecting previously unselected package perl. Preparing to unpack .../04-perl_5.32.1-4+deb11u2_amd64.deb ... Unpacking perl (5.32.1-4+deb11u2) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../05-libaec0_1.0.4-1_amd64.deb ... Unpacking libaec0:amd64 (1.0.4-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../06-libblas3_3.9.0-3+deb11u1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3+deb11u1) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../07-libquadmath0_10.2.1-6_amd64.deb ... Unpacking libquadmath0:amd64 (10.2.1-6) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../08-libgfortran5_10.2.1-6_amd64.deb ... Unpacking libgfortran5:amd64 (10.2.1-6) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../09-liblapack3_3.9.0-3+deb11u1_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-3+deb11u1) ... Selecting previously unselected package libarpack2:amd64. Preparing to unpack .../10-libarpack2_3.8.0-1_amd64.deb ... Unpacking libarpack2:amd64 (3.8.0-1) ... Selecting previously unselected package libsuperlu5:amd64. Preparing to unpack .../11-libsuperlu5_5.2.2+dfsg1-2_amd64.deb ... Unpacking libsuperlu5:amd64 (5.2.2+dfsg1-2) ... Selecting previously unselected package libarmadillo10. Preparing to unpack .../12-libarmadillo10_1%3a10.1.2+dfsg-6+b1_amd64.deb ... Unpacking libarmadillo10 (1:10.1.2+dfsg-6+b1) ... Selecting previously unselected package libboost-program-options1.74.0:amd64. Preparing to unpack .../13-libboost-program-options1.74.0_1.74.0-9_amd64.deb ... Unpacking libboost-program-options1.74.0:amd64 (1.74.0-9) ... Selecting previously unselected package libgzstream0. Preparing to unpack .../14-libgzstream0_1.5+dfsg-5_amd64.deb ... Unpacking libgzstream0 (1.5+dfsg-5) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../15-libsz2_1.0.4-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.4-1) ... Selecting previously unselected package libhdf5-103-1:amd64. Preparing to unpack .../16-libhdf5-103-1_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libtext-csv-perl. Preparing to unpack .../17-libtext-csv-perl_2.00-1_all.deb ... Unpacking libtext-csv-perl (2.00-1) ... Selecting previously unselected package seer. Preparing to unpack .../18-seer_1.1.4-5_amd64.deb ... Unpacking seer (1.1.4-5) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0-9) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u2) ... Setting up libaec0:amd64 (1.0.4-1) ... 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 libquadmath0:amd64 (10.2.1-6) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libgzstream0 (1.5+dfsg-5) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libgdbm6:amd64 (1.19-2) ... 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 libarpack2:amd64 (3.8.0-1) ... Setting up libsuperlu5:amd64 (5.2.2+dfsg1-2) ... 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 libarmadillo10 (1:10.1.2+dfsg-6+b1) ... Setting up perl (5.32.1-4+deb11u2) ... Setting up libtext-csv-perl (2.00-1) ... Setting up seer (1.1.4-5) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer'] 0m7.9s INFO: Running scripts post_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m7.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m8.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpp1qsn703 to bullseye-next 0m8.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m8.4s INFO: Running scripts pre_distupgrade 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'update'] 0m9.9s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [48.4 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://security.debian.org bullseye-security/main amd64 Packages [265 kB] Get:6 http://security.debian.org bullseye-security/main Translation-en [171 kB] Get:7 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [128 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [72.8 kB] Fetched 812 kB in 1s (1012 kB/s) Reading package lists... 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'update'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-yf', 'dist-upgrade'] 0m13.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgnutls30 libperl5.32 perl perl-base perl-modules-5.32 tzdata 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.1 MB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:2 http://security.debian.org bullseye-security/main amd64 libc6 amd64 2.31-13+deb11u7 [2823 kB] Get:3 http://security.debian.org bullseye-security/main amd64 libc-bin amd64 2.31-13+deb11u7 [829 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:5 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl-base amd64 5.32.1-4+deb11u3 [1628 kB] Get:6 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:7 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libgnutls30 amd64 3.7.1-5+deb11u4 [1340 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main amd64 tzdata all 2021a-1+deb11u11 [287 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.1 MB in 0s (152 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8785 files and directories currently installed.) Preparing to unpack .../libperl5.32_5.32.1-4+deb11u3_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../perl_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../perl-base_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.32.1-4+deb11u3) ... (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 ... 8785 files and directories currently installed.) Preparing to unpack .../perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Preparing to unpack .../libc6_2.31-13+deb11u7_amd64.deb ... Unpacking libc6:amd64 (2.31-13+deb11u7) over (2.31-13+deb11u6) ... Setting up libc6:amd64 (2.31-13+deb11u7) ... (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 ... 8785 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-13+deb11u7_amd64.deb ... Unpacking libc-bin (2.31-13+deb11u7) over (2.31-13+deb11u6) ... Setting up libc-bin (2.31-13+deb11u7) ... (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 ... 8785 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u4) over (3.7.1-5+deb11u3) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u4) ... (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 ... 8785 files and directories currently installed.) Preparing to unpack .../tzdata_2021a-1+deb11u11_all.deb ... Unpacking tzdata (2021a-1+deb11u11) over (2021a-1+deb11u10) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u3) ... Setting up tzdata (2021a-1+deb11u11) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 13 05:20:12 UTC 2024. Universal Time is now: Sat Jan 13 05:20:12 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up perl (5.32.1-4+deb11u3) ... Processing triggers for libc-bin (2.31-13+deb11u7) ... 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-yf', 'dist-upgrade'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.5s DUMP: 2b91697b7eeb7089966e9a541af244e9 - 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'show', '--no-all-versions', 'seer'] 0m13.7s DUMP: Package: seer Version: 1.1.4-5 Installed-Size: 4834 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libblas3 | libblas.so.3, libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgzstream0 (>= 1.5+dfsg), libhdf5-103-1, libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), libtext-csv-perl Suggests: fsm-lite Description-en: genomic sequence element (kmer) enrichment analysis Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics. Description-md5: 979255ced90d884824e6cb3db05419ed Homepage: https://github.com/johnlees/seer Section: science Priority: optional Filename: pool/main/s/seer/seer_1.1.4-5_amd64.deb Size: 1176264 MD5sum: 96e6e00be7b9fc6acdbd48002f981451 SHA256: a23129eafa63f6a94ba827b4d801ee79ff1ab0983ca2b9f785c8c0b24bf3c242 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'show', '--no-all-versions', 'seer'] 0m13.7s INFO: apt-cache knows about the following packages: seer 0m13.7s INFO: Running scripts pre_install 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m13.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 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: 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m13.8s DUMP: seer: Installed: 1.1.4-5 Candidate: 1.1.4-5 Version table: *** 1.1.4-5 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer'] 0m14.2s DUMP: Reading package lists... Building dependency tree... Reading state information... seer is already the newest version (1.1.4-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer'] 0m14.2s INFO: Running scripts post_install 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m14.2s INFO: Running scripts post_distupgrade 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m14.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m15.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m15.4s INFO: Running scripts pre_install 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_database-server'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_exceptions'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_extras'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m15.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 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: 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m15.5s DUMP: seer: Installed: 1.1.4-5 Candidate: 1.1.4-5 Version table: *** 1.1.4-5 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-cache', 'policy', 'seer'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer=1.1.4-5'] 0m15.8s DUMP: Reading package lists... Building dependency tree... Reading state information... seer is already the newest version (1.1.4-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', '-y', 'install', 'seer=1.1.4-5'] 0m15.8s INFO: Running scripts post_install 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_install_exceptions'] 0m15.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m16.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m16.4s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m16.4s INFO: /bin converted to /usr/bin by /usr merge 0m16.4s INFO: /lib converted to /usr/lib by /usr merge 0m16.4s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m16.4s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m16.4s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m16.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m16.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m16.4s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m16.4s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m16.4s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m16.4s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m16.4s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m16.4s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m16.4s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m16.4s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m16.4s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m16.4s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m16.4s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m16.4s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m16.4s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m16.4s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m16.4s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m16.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m16.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m16.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m16.4s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m16.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m16.4s INFO: /sbin converted to /usr/sbin by /usr merge 0m16.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', '-ac', '--ignore-obsolete'] 0m17.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', '-ac', '--ignore-obsolete'] 0m17.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m17.7s DUMP: 0.15.6 0m17.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m17.7s INFO: Running adequate version 0.15.6 now. 0m17.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'seer'] 0m17.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'seer'] 0m17.9s INFO: Running scripts pre_remove 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/pre_remove_exceptions'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.2s 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 libaec0:amd64 libaec0 1.0.4-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libarmadillo10 libarmadillo10 1:10.1.2+dfsg-6+b1 install ok installed libarpack2:amd64 libarpack2 3.8.0-1 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 libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0-9 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u7 install ok installed libc6:amd64 libc6 2.31-13+deb11u7 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 libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 install ok installed libgfortran5:amd64 libgfortran5 10.2.1-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 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 libgzstream0 libgzstream0 1.5+dfsg-5 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.6+repack-4+deb11u1 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 liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 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 libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libquadmath0:amd64 libquadmath0 10.2.1-6 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 libsuperlu5:amd64 libsuperlu5 5.2.2+dfsg1-2 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libsz2:amd64 libsz2 1.0.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtext-csv-perl libtext-csv-perl 2.00-1 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 perl 5.32.1-4+deb11u3 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed seer seer 1.1.4-5 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+deb11u11 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 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'remove', 'libaec0:amd64', 'libarmadillo10', 'libarpack2:amd64', 'libblas3:amd64', 'libboost-program-options1.74.0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgzstream0', 'libhdf5-103-1:amd64', 'liblapack3:amd64', 'libperl5.32:amd64', 'libquadmath0:amd64', 'libsuperlu5:amd64', 'libsz2:amd64', 'libtext-csv-perl', 'perl', 'perl-modules-5.32', 'seer'] 0m19.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libarmadillo10 libarpack2 libblas3 libboost-program-options1.74.0 libgdbm-compat4 libgdbm6 libgfortran5 libgzstream0 libhdf5-103-1 liblapack3 libperl5.32 libquadmath0 libsuperlu5 libsz2 libtext-csv-perl perl perl-modules-5.32 seer 0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded. After this operation, 71.3 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 ... 8785 files and directories currently installed.) Removing seer (1.1.4-5) ... Removing libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Removing libsz2:amd64 (1.0.4-1) ... Removing libaec0:amd64 (1.0.4-1) ... Removing libarmadillo10 (1:10.1.2+dfsg-6+b1) ... Removing libarpack2:amd64 (3.8.0-1) ... Removing libsuperlu5:amd64 (5.2.2+dfsg1-2) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing libboost-program-options1.74.0:amd64 (1.74.0-9) ... Removing libtext-csv-perl (2.00-1) ... Removing perl (5.32.1-4+deb11u3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing libgzstream0 (1.5+dfsg-5) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Processing triggers for libc-bin (2.31-13+deb11u7) ... 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'remove', 'libaec0:amd64', 'libarmadillo10', 'libarpack2:amd64', 'libblas3:amd64', 'libboost-program-options1.74.0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgzstream0', 'libhdf5-103-1:amd64', 'liblapack3:amd64', 'libperl5.32:amd64', 'libquadmath0:amd64', 'libsuperlu5:amd64', 'libsz2:amd64', 'libtext-csv-perl', 'perl', 'perl-modules-5.32', 'seer'] 0m19.8s INFO: Running scripts post_remove 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_remove_exceptions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_remove_exceptions'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', 'libaec0:amd64', 'libarmadillo10', 'libarpack2:amd64', 'libblas3:amd64', 'libboost-program-options1.74.0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgzstream0', 'libhdf5-103-1:amd64', 'liblapack3:amd64', 'libperl5.32:amd64', 'libquadmath0:amd64', 'libsuperlu5:amd64', 'libsz2:amd64', 'libtext-csv-perl', 'perl', 'perl-modules-5.32'] 0m19.8s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libarmadillo10 which isn't installed dpkg: warning: ignoring request to remove libarpack2 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.74.0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgzstream0 which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libsuperlu5 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed (Reading database ... 6669 files and directories currently installed.) Purging configuration files for perl (5.32.1-4+deb11u3) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', 'libaec0:amd64', 'libarmadillo10', 'libarpack2:amd64', 'libblas3:amd64', 'libboost-program-options1.74.0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgzstream0', 'libhdf5-103-1:amd64', 'liblapack3:amd64', 'libperl5.32:amd64', 'libquadmath0:amd64', 'libsuperlu5:amd64', 'libsz2:amd64', 'libtext-csv-perl', 'perl', 'perl-modules-5.32'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', 'seer'] 0m19.8s DUMP: dpkg: warning: ignoring request to remove seer which isn't installed 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', 'seer'] 0m19.8s INFO: Running scripts post_purge 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_purge_exceptions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_purge_exceptions'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', '--pending'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--purge', '--pending'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--remove', '--pending'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg', '--remove', '--pending'] 0m19.8s INFO: Running scripts post_test 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_test_exceptions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'tmp/scripts/post_test_exceptions'] 0m19.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m20.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-divert', '--list'] 0m20.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'dpkg-divert', '--list'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'clean'] 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp1qsn703', 'apt-get', 'clean'] 0m20.3s DEBUG: Recording chroot state 0m21.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/shm'] 0m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/shm'] 0m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/console'] 0m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/console'] 0m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/ptmx'] 0m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/ptmx'] 0m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts'] 0m21.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/dev/pts'] 0m21.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/proc'] 0m21.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp1qsn703/proc'] 0m21.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m21.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpp1qsn703'] 0m21.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpp1qsn703 0m21.4s INFO: PASS: Upgrading between Debian distributions. 0m21.4s INFO: PASS: All tests. 0m21.4s INFO: piuparts run ends. ret=0 End: 2024-01-13 05:20:20 GMT