Start: 2024-12-14 03:09:50 GMT [testing] Package: baitfisher Version: 1.2.7+git20211020.de26d5c+dfsg-1 Installed-Size: 642 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.0), libstdc++6 (>= 11) Description: software package for designing hybrid enrichment probes Homepage: https://github.com/cmayer/BaitFisher-package Description-md5: 4f8112acea1615fb8dd7625fdf2f7898 Section: science Priority: optional Filename: pool/main/b/baitfisher/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_amd64.deb Size: 200748 MD5sum: 74843c77b91a71061c58595fae4af0cf SHA256: 3861b82b9badb409175df5410435d1e4cba0006a2c17af96f13e5086e6f135ce [sid] Package: baitfisher Version: 1.2.7+git20211020.de26d5c+dfsg-2 Installed-Size: 674 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 14) Description: software package for designing hybrid enrichment probes Homepage: https://github.com/cmayer/BaitFisher-package Description-md5: 4f8112acea1615fb8dd7625fdf2f7898 Section: science Priority: optional Filename: pool/main/b/baitfisher/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb Size: 216776 MD5sum: 6b3f35f40d3bd96da06681240c4df2cd SHA256: dc366a0b09efd89400718f579c90938d40bcd1301a2651ab648ab849209bd614 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt baitfisher=1.2.7+git20211020.de26d5c+dfsg-2 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt baitfisher=1.2.7+git20211020.de26d5c+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp_i78j6bz 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_i78j6bz 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_i78j6bz/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'update'] 0m1.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9354 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6280 kB] Fetched 15.8 MB in 1s (20.5 MB/s) Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libsystemd0 libudev1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 595 kB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257-2 [448 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257-2 [147 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 595 kB in 0s (25.6 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 ... 5137 files and directories currently installed.) Preparing to unpack .../libsystemd0_257-2_amd64.deb ... Unpacking libsystemd0:amd64 (257-2) over (257~rc3-1) ... Setting up libsystemd0:amd64 (257-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5137 files and directories currently installed.) Preparing to unpack .../libudev1_257-2_amd64.deb ... Unpacking libudev1:amd64 (257-2) over (257~rc3-1) ... Setting up libudev1:amd64 (257-2) ... Processing triggers for libc-bin (2.40-4) ... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.1s DUMP: 089610de4facafad7ebe90f4e26170b1 - 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s 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 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.16 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257-2 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m2.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m2.7s INFO: Running scripts is_testable 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/is_testable_uninstallable'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/is_testable_uninstallable'] 0m2.7s INFO: Running scripts pre_test 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_test_exceptions'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_test_exceptions'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_test_root_password'] 0m2.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_test_root_password'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m2.9s DUMP: Package: baitfisher Version: 1.2.7+git20211020.de26d5c+dfsg-1 Installed-Size: 642 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.0), libstdc++6 (>= 11) Description-en: software package for designing hybrid enrichment probes The BaitFisher package consists of two programs: BaitFisher and BaitFilter. . BaitFisher was been designed to construct hybrid enrichment baits from multiple sequence alignments (MSAs) or annotated features in MSAs. The main goal of BaitFisher is to avoid redundancy in the construction of baits by designing fewer baits in conserved regions of the MSAs and designing more baits in variable regions. This makes use of the fact that hybrid enrichment baits can differ to some extends from the target region, which they should capture in the enrichment procedure. By specifying the allowed distance between baits and the sequences in the MSAs the user can control the allowed bait-to-target distance and the degree of reduction in the number of baits that are designed. See the BaitFisher paper for details. . BaitFilter was designed (i) to determine whether baits bind unspecifically to a reference genome, (ii) to filter baits that only have partial length matches to a reference genome, (iii) to determine the optimal bait region in a MSA and to convert baits to a format that can be uploaded at a bait constructing company. The optimal bait region can be the most conserved region in the MSA or the region with the highest number of sequences without gaps or ambiguous nucleotides. Description-md5: 4f8112acea1615fb8dd7625fdf2f7898 Homepage: https://github.com/cmayer/BaitFisher-package Section: science Priority: optional Filename: pool/main/b/baitfisher/baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_amd64.deb Size: 200748 MD5sum: 74843c77b91a71061c58595fae4af0cf SHA256: 3861b82b9badb409175df5410435d1e4cba0006a2c17af96f13e5086e6f135ce 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m2.9s INFO: apt-cache knows about the following packages: baitfisher 0m2.9s INFO: Running scripts pre_install 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m2.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m2.9s DUMP: baitfisher: Installed: (none) Candidate: 1.2.7+git20211020.de26d5c+dfsg-1 Version table: 1.2.7+git20211020.de26d5c+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher'] 0m3.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: baitfisher 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 201 kB of archives. After this operation, 657 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 baitfisher amd64 1.2.7+git20211020.de26d5c+dfsg-1 [201 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 201 kB in 0s (1260 kB/s) Selecting previously unselected package baitfisher. (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 ... 5141 files and directories currently installed.) Preparing to unpack .../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_amd64.deb ... Unpacking baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) ... Setting up baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) ... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher'] 0m3.4s INFO: Running scripts post_install 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m3.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp_i78j6bz to sid 0m3.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m3.7s INFO: Running scripts pre_distupgrade 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'update'] 0m5.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7348 kB] Fetched 17.6 MB in 1s (12.7 MB/s) Reading package lists... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'update'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt baitfisher libapt-pkg6.0t64 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2698 kB of archives. After this operation, 36.9 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.17 [1113 kB] Get:2 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.17 [1368 kB] Get:3 http://deb.debian.org/debian sid/main amd64 baitfisher amd64 1.2.7+git20211020.de26d5c+dfsg-2 [217 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2698 kB in 0s (82.0 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 ... 5159 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.17_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.17) over (2.9.16) ... Setting up libapt-pkg6.0t64:amd64 (2.9.17) ... (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 ... 5159 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.17_amd64.deb ... Unpacking apt (2.9.17) over (2.9.16) ... Setting up apt (2.9.17) ... (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 ... 5153 files and directories currently installed.) Preparing to unpack .../baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb ... Unpacking baitfisher (1.2.7+git20211020.de26d5c+dfsg-2) over (1.2.7+git20211020.de26d5c+dfsg-1) ... Setting up baitfisher (1.2.7+git20211020.de26d5c+dfsg-2) ... Processing triggers for libc-bin (2.40-4) ... 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-yf', 'dist-upgrade'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s DUMP: e05d3afc8dc07dd9f827650e94ebfaaa - 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m7.0s DUMP: Package: baitfisher Version: 1.2.7+git20211020.de26d5c+dfsg-2 Installed-Size: 674 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 14) Description-en: software package for designing hybrid enrichment probes The BaitFisher package consists of two programs: BaitFisher and BaitFilter. . BaitFisher was been designed to construct hybrid enrichment baits from multiple sequence alignments (MSAs) or annotated features in MSAs. The main goal of BaitFisher is to avoid redundancy in the construction of baits by designing fewer baits in conserved regions of the MSAs and designing more baits in variable regions. This makes use of the fact that hybrid enrichment baits can differ to some extends from the target region, which they should capture in the enrichment procedure. By specifying the allowed distance between baits and the sequences in the MSAs the user can control the allowed bait-to-target distance and the degree of reduction in the number of baits that are designed. See the BaitFisher paper for details. . BaitFilter was designed (i) to determine whether baits bind unspecifically to a reference genome, (ii) to filter baits that only have partial length matches to a reference genome, (iii) to determine the optimal bait region in a MSA and to convert baits to a format that can be uploaded at a bait constructing company. The optimal bait region can be the most conserved region in the MSA or the region with the highest number of sequences without gaps or ambiguous nucleotides. Description-md5: 4f8112acea1615fb8dd7625fdf2f7898 Homepage: https://github.com/cmayer/BaitFisher-package Section: science Priority: optional Filename: pool/main/b/baitfisher/baitfisher_1.2.7+git20211020.de26d5c+dfsg-2_amd64.deb Size: 216776 MD5sum: 6b3f35f40d3bd96da06681240c4df2cd SHA256: dc366a0b09efd89400718f579c90938d40bcd1301a2651ab648ab849209bd614 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m7.0s INFO: apt-cache knows about the following packages: baitfisher 0m7.0s INFO: Running scripts pre_install 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m7.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m7.1s DUMP: baitfisher: Installed: 1.2.7+git20211020.de26d5c+dfsg-2 Candidate: 1.2.7+git20211020.de26d5c+dfsg-2 Version table: *** 1.2.7+git20211020.de26d5c+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher'] 0m7.3s DUMP: Reading package lists... Building dependency tree... Reading state information... baitfisher is already the newest version (1.2.7+git20211020.de26d5c+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher'] 0m7.3s INFO: Running scripts post_install 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m7.3s INFO: Running scripts post_distupgrade 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_exceptions'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_zz_backports'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_distupgrade_zz_backports'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m7.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m7.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m7.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m7.8s INFO: Running scripts pre_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_database-server'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_extras'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m7.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m7.9s DUMP: baitfisher: Installed: 1.2.7+git20211020.de26d5c+dfsg-2 Candidate: 1.2.7+git20211020.de26d5c+dfsg-2 Version table: *** 1.2.7+git20211020.de26d5c+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-cache', 'policy', 'baitfisher'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher=1.2.7+git20211020.de26d5c+dfsg-2'] 0m8.1s DUMP: Reading package lists... Building dependency tree... Reading state information... baitfisher is already the newest version (1.2.7+git20211020.de26d5c+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', '-y', 'install', 'baitfisher=1.2.7+git20211020.de26d5c+dfsg-2'] 0m8.1s INFO: Running scripts post_install 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_install_exceptions'] 0m8.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m8.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m8.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', '-ac', '--ignore-obsolete'] 0m8.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', '-ac', '--ignore-obsolete'] 0m8.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.8s DUMP: 0.15.6 0m8.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.8s INFO: Running adequate version 0.15.6 now. 0m8.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'baitfisher'] 0m8.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'baitfisher'] 0m8.9s INFO: Running scripts pre_remove 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_exceptions'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/pre_remove_exceptions'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.2s DUMP: install ok installed apt apt 2.9.17 install ok installed baitfisher baitfisher 1.2.7+git20211020.de26d5c+dfsg-2 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.17 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257-2 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'remove', 'baitfisher'] 0m9.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: baitfisher 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 690 kB 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 ... 5153 files and directories currently installed.) Removing baitfisher (1.2.7+git20211020.de26d5c+dfsg-2) ... 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'remove', 'baitfisher'] 0m9.6s INFO: Running scripts post_remove 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_remove_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_remove_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--purge', 'baitfisher'] 0m9.6s DUMP: dpkg: warning: ignoring request to remove baitfisher which isn't installed 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--purge', 'baitfisher'] 0m9.6s INFO: Running scripts post_purge 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_purge_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_purge_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--purge', '--pending'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--purge', '--pending'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--remove', '--pending'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg', '--remove', '--pending'] 0m9.6s INFO: Running scripts post_test 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_test_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'tmp/scripts/post_test_exceptions'] 0m9.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m9.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-divert', '--list'] 0m9.9s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'dpkg-divert', '--list'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'clean'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz', 'apt-get', 'clean'] 0m9.9s DEBUG: Recording chroot state 0m10.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/shm'] 0m10.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/shm'] 0m10.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/console'] 0m10.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/console'] 0m10.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/ptmx'] 0m10.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/ptmx'] 0m10.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts'] 0m10.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/dev/pts'] 0m10.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/proc'] 0m10.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz/proc'] 0m10.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m10.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_i78j6bz'] 0m10.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_i78j6bz 0m10.5s INFO: PASS: Upgrading between Debian distributions. 0m10.5s INFO: PASS: All tests. 0m10.5s INFO: piuparts run ends. ret=0 End: 2024-12-14 03:10:00 GMT