Start: 2022-01-16 21:00:11 GMT [testing] Package: baitfisher Version: 1.2.7+git20190123.241d060+dfsg-1 Installed-Size: 630 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) 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+git20190123.241d060+dfsg-1_amd64.deb Size: 193608 MD5sum: 0e726dd83df981111f1db566789a3bc8 SHA256: 90c4509f4fd72804b37504b9fd75ce7b5aea0553804f79d654759fa06b071104 [sid] 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 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt baitfisher=1.2.7+git20211020.de26d5c+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.4 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt baitfisher=1.2.7+git20211020.de26d5c+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-18-amd64 #1 SMP Debian 4.19.208-1 (2021-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmppb2lcvpp 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppb2lcvpp 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmppb2lcvpp/tmp/scripts/ 0m2.4s INFO: Running scripts post_chroot_unpack 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'update'] 0m6.5s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [129 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8248 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5668 kB] Fetched 14.0 MB in 3s (4662 kB/s) Reading package lists... 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'update'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-yf', 'dist-upgrade'] 0m9.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash libc-bin libc6 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5072 kB of archives. After this operation, 1024 B disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.1-6 [1411 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.33-2 [2827 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.33-2 [834 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5072 kB in 0s (46.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6675 files and directories currently installed.) Preparing to unpack .../archives/bash_5.1-6_amd64.deb ... Unpacking bash (5.1-6) over (5.1-5+b1) ... Setting up bash (5.1-6) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6674 files and directories currently installed.) Preparing to unpack .../libc6_2.33-2_amd64.deb ... Unpacking libc6:amd64 (2.33-2) over (2.33-1) ... Setting up libc6:amd64 (2.33-2) ... (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 ... 6674 files and directories currently installed.) Preparing to unpack .../libc-bin_2.33-2_amd64.deb ... Unpacking libc-bin (2.33-2) over (2.33-1) ... Setting up libc-bin (2.33-2) ... 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-yf', 'dist-upgrade'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.7s DUMP: e7b897083510b7cfc82152bd420994d9 - 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.7s INFO: Running scripts post_setup 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_dummy_users'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_dummy_users'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_forbid_home'] 0m11.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_forbid_home'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_minimize'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_minimize'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_zz_backports'] 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_setup_zz_backports'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.3.14 install ok installed base-files base-files 12 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.2-5 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-3 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.1 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.3.0-13 install ok installed gcc-11-base:amd64 gcc-11-base 11.2.0-13 install ok installed gpgv gpgv 2.2.27-3 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.61 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.3.14 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.6-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.6-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.2-5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-2 install ok installed libc6:amd64 libc6 2.33-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-3 install ok installed libgcc-s1:amd64 libgcc-s1 11.2.0-13 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.2-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-7 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-7 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-7 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-7 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.2-5 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b1 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b1 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.2-5 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1m-1 install ok installed libstdc++6:amd64 libstdc++6 11.2.0-13 install ok installed libsystemd0:amd64 libsystemd0 249.7-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-1 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 249.7-1 install ok installed libunistring2:amd64 libunistring2 0.9.10-6 install ok installed libuuid1:amd64 libuuid1 2.37.2-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-3 install ok installed login login 1:4.8.1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.37.2-5 install ok installed ncurses-base ncurses-base 6.3-1 install ok installed ncurses-bin ncurses-bin 6.3-1 install ok installed passwd passwd 1:4.8.1-2 install ok installed perl-base perl-base 5.32.1-6 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021e-1 install ok installed util-linux util-linux 2.37.2-5 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m11.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m11.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m11.7s INFO: Running scripts is_testable 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/is_testable_uninstallable'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/is_testable_uninstallable'] 0m11.7s INFO: Running scripts pre_test 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_test_exceptions'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_test_exceptions'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_test_root_password'] 0m11.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_test_root_password'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m12.0s DUMP: Package: baitfisher Version: 1.2.7+git20190123.241d060+dfsg-1 Installed-Size: 630 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) 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+git20190123.241d060+dfsg-1_amd64.deb Size: 193608 MD5sum: 0e726dd83df981111f1db566789a3bc8 SHA256: 90c4509f4fd72804b37504b9fd75ce7b5aea0553804f79d654759fa06b071104 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m12.0s INFO: apt-cache knows about the following packages: baitfisher 0m12.0s INFO: Running scripts pre_install 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m12.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m12.1s DUMP: baitfisher: Installed: (none) Candidate: 1.2.7+git20190123.241d060+dfsg-1 Version table: 1.2.7+git20190123.241d060+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher'] 0m13.2s 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 194 kB of archives. After this operation, 645 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 baitfisher amd64 1.2.7+git20190123.241d060+dfsg-1 [194 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 194 kB in 0s (5873 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 ... 6676 files and directories currently installed.) Preparing to unpack .../baitfisher_1.2.7+git20190123.241d060+dfsg-1_amd64.deb ... Unpacking baitfisher (1.2.7+git20190123.241d060+dfsg-1) ... Setting up baitfisher (1.2.7+git20190123.241d060+dfsg-1) ... 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher'] 0m13.2s INFO: Running scripts post_install 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m13.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m13.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m13.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmppb2lcvpp to sid 0m13.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m13.5s INFO: Running scripts pre_distupgrade 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'update'] 0m19.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [165 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8885 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6668 kB] Fetched 15.7 MB in 4s (3865 kB/s) Reading package lists... 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'update'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: baitfisher bsdutils debianutils gcc-10-base gcc-11-base libblkid1 libgcc-s1 libgpg-error0 libmount1 libsmartcols1 libstdc++6 libsystemd0 libudev1 libuuid1 libxxhash0 mount util-linux 17 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4218 kB of archives. After this operation, 125 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.37.2-6 [149 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.5-1 [93.7 kB] Get:3 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.37.2-6 [1198 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 250.2-3 [401 kB] Get:5 http://deb.debian.org/debian sid/main amd64 mount amd64 2.37.2-6 [190 kB] Get:6 http://deb.debian.org/debian sid/main amd64 gcc-11-base amd64 11.2.0-14 [207 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-14 [577 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 11.2.0-14 [42.0 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.37.2-6 [201 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.43-2 [82.2 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.37.2-6 [219 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.37.2-6 [161 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 250.2-3 [176 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.37.2-6 [85.1 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:16 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.3.0-14 [206 kB] Get:17 http://deb.debian.org/debian sid/main amd64 baitfisher amd64 1.2.7+git20211020.de26d5c+dfsg-1 [201 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4218 kB in 0s (38.7 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6690 files and directories currently installed.) Preparing to unpack .../gcc-10-base_10.3.0-14_amd64.deb ... Unpacking gcc-10-base:amd64 (10.3.0-14) over (10.3.0-13) ... Preparing to unpack .../baitfisher_1.2.7+git20211020.de26d5c+dfsg-1_amd64.deb ... Unpacking baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) over (1.2.7+git20190123.241d060+dfsg-1) ... Setting up gcc-10-base:amd64 (10.3.0-14) ... Setting up mount (2.37.2-6) ... Setting up baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) ... Processing triggers for libc-bin (2.33-2) ... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.4s DUMP: 0f8ad17f89344e1a6766ba6988a074e8 - 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m22.8s 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 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'show', '--no-all-versions', 'baitfisher'] 0m22.8s INFO: apt-cache knows about the following packages: baitfisher 0m22.8s INFO: Running scripts pre_install 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m23.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m23.0s DUMP: baitfisher: Installed: 1.2.7+git20211020.de26d5c+dfsg-1 Candidate: 1.2.7+git20211020.de26d5c+dfsg-1 Version table: *** 1.2.7+git20211020.de26d5c+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher'] 0m23.8s DUMP: Reading package lists... Building dependency tree... Reading state information... baitfisher is already the newest version (1.2.7+git20211020.de26d5c+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher'] 0m23.8s INFO: Running scripts post_install 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m23.8s INFO: Running scripts post_distupgrade 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m24.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m24.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m24.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m24.8s INFO: Running scripts pre_install 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_database-server'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_extras'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m24.9s 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: 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m25.0s DUMP: baitfisher: Installed: 1.2.7+git20211020.de26d5c+dfsg-1 Candidate: 1.2.7+git20211020.de26d5c+dfsg-1 Version table: *** 1.2.7+git20211020.de26d5c+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-cache', 'policy', 'baitfisher'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher=1.2.7+git20211020.de26d5c+dfsg-1'] 0m25.8s DUMP: Reading package lists... Building dependency tree... Reading state information... baitfisher is already the newest version (1.2.7+git20211020.de26d5c+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', '-y', 'install', 'baitfisher=1.2.7+git20211020.de26d5c+dfsg-1'] 0m25.8s INFO: Running scripts post_install 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_install_exceptions'] 0m25.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m26.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m26.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', '-ac', '--ignore-obsolete'] 0m27.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', '-ac', '--ignore-obsolete'] 0m27.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m27.8s DUMP: 0.15.2 0m27.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m27.8s INFO: Running adequate version 0.15.2 now. 0m27.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'baitfisher'] 0m27.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'baitfisher'] 0m27.9s INFO: Running scripts pre_remove 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_exceptions'] 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/pre_remove_exceptions'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m29.4s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.3.14 install ok installed baitfisher baitfisher 1.2.7+git20211020.de26d5c+dfsg-1 install ok installed base-files base-files 12 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.2-6 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-3 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.5-1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.1 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.3.0-14 install ok installed gcc-11-base:amd64 gcc-11-base 11.2.0-14 install ok installed gpgv gpgv 2.2.27-3 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.61 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.3.14 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.6-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.6-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-2 install ok installed libc6:amd64 libc6 2.33-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-3 install ok installed libgcc-s1:amd64 libgcc-s1 11.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.2-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-7 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-7 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-7 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-7 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.2-6 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b1 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b1 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.2-6 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1m-1 install ok installed libstdc++6:amd64 libstdc++6 11.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 250.2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-1 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 250.2-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-6 install ok installed libuuid1:amd64 libuuid1 2.37.2-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-3 install ok installed login login 1:4.8.1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.37.2-6 install ok installed ncurses-base ncurses-base 6.3-1 install ok installed ncurses-bin ncurses-bin 6.3-1 install ok installed passwd passwd 1:4.8.1-2 install ok installed perl-base perl-base 5.32.1-6 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021e-1 install ok installed util-linux util-linux 2.37.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'remove', 'baitfisher'] 0m30.5s 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, 657 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 ... 6690 files and directories currently installed.) Removing baitfisher (1.2.7+git20211020.de26d5c+dfsg-1) ... 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'remove', 'baitfisher'] 0m30.5s INFO: Running scripts post_remove 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_remove_exceptions'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_remove_exceptions'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--purge', 'baitfisher'] 0m30.6s DUMP: dpkg: warning: ignoring request to remove baitfisher which isn't installed 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--purge', 'baitfisher'] 0m30.6s INFO: Running scripts post_purge 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_purge_exceptions'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_purge_exceptions'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--purge', '--pending'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--purge', '--pending'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--remove', '--pending'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg', '--remove', '--pending'] 0m30.6s INFO: Running scripts post_test 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_test_exceptions'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'tmp/scripts/post_test_exceptions'] 0m30.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m31.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-divert', '--list'] 0m31.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'dpkg-divert', '--list'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'clean'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp', 'apt-get', 'clean'] 0m31.1s DEBUG: Recording chroot state 0m32.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/shm'] 0m32.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/shm'] 0m32.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/console'] 0m32.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/console'] 0m32.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/ptmx'] 0m32.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/ptmx'] 0m32.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts'] 0m32.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/dev/pts'] 0m32.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/proc'] 0m32.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp/proc'] 0m32.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m32.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppb2lcvpp'] 0m32.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppb2lcvpp 0m32.3s INFO: PASS: Upgrading between Debian distributions. 0m32.3s INFO: PASS: All tests. 0m32.3s INFO: piuparts run ends. ret=0 End: 2022-01-16 21:00:43 GMT