Start: 2024-08-22 03:31:22 GMT [bookworm] Package: exonerate Version: 2.4.0-5 Installed-Size: 8240 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description: generic tool for pairwise sequence comparison Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.4.0-5_amd64.deb Size: 1616012 MD5sum: 33296213d7595a9a7ab335813c5dd643 SHA256: e6d8648b051abdae50e79d300614f572d03dfbcd877670e089fc1bb389470fd6 [bookworm-next] Package: exonerate Version: 2.4.0-5 Installed-Size: 8240 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description: generic tool for pairwise sequence comparison Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Description-md5: 61984be320e7cae47c75d879b270d329 Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.4.0-5_amd64.deb Size: 1616012 MD5sum: 33296213d7595a9a7ab335813c5dd643 SHA256: e6d8648b051abdae50e79d300614f572d03dfbcd877670e089fc1bb389470fd6 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/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt exonerate=2.4.0-5 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 1.4.4~202408201642~1.4.3-11-g36a88c35 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/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt exonerate=2.4.0-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp1ix58m3b 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp1ix58m3b 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/9', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/9', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp1ix58m3b/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'update'] 0m1.5s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.2s INFO: Running scripts post_setup 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_zz_backports'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_setup_zz_backports'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.0s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_test_root_password'] 0m3.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_test_root_password'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m3.5s DUMP: Package: exonerate Version: 2.4.0-5 Installed-Size: 8240 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description-en: generic tool for pairwise sequence comparison Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. . An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. . This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb Description-md5: 61984be320e7cae47c75d879b270d329 Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.4.0-5_amd64.deb Size: 1616012 MD5sum: 33296213d7595a9a7ab335813c5dd643 SHA256: e6d8648b051abdae50e79d300614f572d03dfbcd877670e089fc1bb389470fd6 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m3.5s INFO: apt-cache knows about the following packages: exonerate 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m3.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m3.6s DUMP: exonerate: Installed: (none) Candidate: 2.4.0-5 Version table: 2.4.0-5 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate'] 0m4.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libglib2.0-0 Suggested packages: wise low-memory-monitor Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs The following NEW packages will be installed: exonerate libglib2.0-0 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 3016 kB of archives. After this operation, 12.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 exonerate amd64 2.4.0-5 [1616 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3016 kB in 0s (21.3 MB/s) Selecting previously unselected package libglib2.0-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6093 files and directories currently installed.) Preparing to unpack .../libglib2.0-0_2.74.6-2+deb12u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Selecting previously unselected package exonerate. Preparing to unpack .../exonerate_2.4.0-5_amd64.deb ... Unpacking exonerate (2.4.0-5) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up exonerate (2.4.0-5) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate'] 0m4.6s INFO: Running scripts post_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m4.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp1ix58m3b to bookworm-next 0m4.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m4.9s INFO: Running scripts pre_distupgrade 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'update'] 0m6.2s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [108 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [61.8 kB] Fetched 644 kB in 1s (874 kB/s) Reading package lists... 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'update'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libsystemd0 libudev1 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3803 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:3 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3803 kB in 0s (62.9 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 ... 6216 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 6216 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (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 ... 6216 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (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 ... 6216 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.7s DUMP: 1ca3138f5e2a7360395f9364c839e53e - 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m8.9s DUMP: Package: exonerate Version: 2.4.0-5 Installed-Size: 8240 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libglib2.0-0 (>= 2.24.0) Suggests: wise Enhances: bioperl-run Description-en: generic tool for pairwise sequence comparison Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general. . An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate. . This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb Description-md5: 61984be320e7cae47c75d879b270d329 Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::TODO, use::searching, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/e/exonerate/exonerate_2.4.0-5_amd64.deb Size: 1616012 MD5sum: 33296213d7595a9a7ab335813c5dd643 SHA256: e6d8648b051abdae50e79d300614f572d03dfbcd877670e089fc1bb389470fd6 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'show', '--no-all-versions', 'exonerate'] 0m8.9s INFO: apt-cache knows about the following packages: exonerate 0m8.9s INFO: Running scripts pre_install 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m9.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m9.1s DUMP: exonerate: Installed: 2.4.0-5 Candidate: 2.4.0-5 Version table: *** 2.4.0-5 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate'] 0m9.6s DUMP: Reading package lists... Building dependency tree... Reading state information... exonerate is already the newest version (2.4.0-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate'] 0m9.6s INFO: Running scripts post_install 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m9.6s INFO: Running scripts post_distupgrade 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_zz_backports'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_distupgrade_zz_backports'] 0m9.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m10.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m10.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m10.4s INFO: Running scripts pre_install 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_database-server'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_exceptions'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_extras'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m10.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m10.7s DUMP: exonerate: Installed: 2.4.0-5 Candidate: 2.4.0-5 Version table: *** 2.4.0-5 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-cache', 'policy', 'exonerate'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate=2.4.0-5'] 0m11.1s DUMP: Reading package lists... Building dependency tree... Reading state information... exonerate is already the newest version (2.4.0-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', '-y', 'install', 'exonerate=2.4.0-5'] 0m11.1s INFO: Running scripts post_install 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_install_exceptions'] 0m11.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m11.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m11.6s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m11.6s INFO: /bin converted to /usr/bin by /usr merge 0m11.6s INFO: /lib converted to /usr/lib by /usr merge 0m11.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m11.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m11.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m11.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m11.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m11.6s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m11.6s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m11.6s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m11.6s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m11.6s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m11.6s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m11.6s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m11.6s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m11.6s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m11.6s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m11.6s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m11.6s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m11.6s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m11.6s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m11.6s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m11.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m11.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m11.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m11.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m11.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m11.6s INFO: /sbin converted to /usr/sbin by /usr merge 0m11.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', '-ac', '--ignore-obsolete'] 0m12.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', '-ac', '--ignore-obsolete'] 0m12.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.7s DUMP: 0.15.6 0m12.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.7s INFO: Running adequate version 0.15.6 now. 0m12.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'exonerate'] 0m13.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'exonerate'] 0m13.2s INFO: Running scripts pre_remove 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_exceptions'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/pre_remove_exceptions'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed exonerate exonerate 2.4.0-5 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'remove', 'libglib2.0-0:amd64', 'exonerate'] 0m14.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: exonerate libglib2.0-0 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. After this operation, 12.7 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 ... 6216 files and directories currently installed.) Removing exonerate (2.4.0-5) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'remove', 'libglib2.0-0:amd64', 'exonerate'] 0m14.7s INFO: Running scripts post_remove 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_remove_exceptions'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_remove_exceptions'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', 'libglib2.0-0:amd64'] 0m14.7s DUMP: (Reading database ... 6093 files and directories currently installed.) Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', 'libglib2.0-0:amd64'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', 'exonerate'] 0m14.8s DUMP: dpkg: warning: ignoring request to remove exonerate which isn't installed 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', 'exonerate'] 0m14.8s INFO: Running scripts post_purge 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_purge_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_purge_exceptions'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', '--pending'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--purge', '--pending'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--remove', '--pending'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg', '--remove', '--pending'] 0m14.8s INFO: Running scripts post_test 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_test_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'tmp/scripts/post_test_exceptions'] 0m14.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m15.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-divert', '--list'] 0m15.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'dpkg-divert', '--list'] 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'clean'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b', 'apt-get', 'clean'] 0m15.4s DEBUG: Recording chroot state 0m16.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/shm'] 0m16.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/shm'] 0m16.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/console'] 0m16.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/console'] 0m16.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/ptmx'] 0m16.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/ptmx'] 0m16.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts'] 0m16.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/dev/pts'] 0m16.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/proc'] 0m16.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b/proc'] 0m16.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m16.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1ix58m3b'] 0m16.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp1ix58m3b 0m16.5s INFO: PASS: Upgrading between Debian distributions. 0m16.5s INFO: PASS: All tests. 0m16.5s INFO: piuparts run ends. ret=0 End: 2024-08-22 03:31:39 GMT