Start: 2023-01-10 15:54:25 GMT [testing] Package: any2fasta-examples Source: any2fasta Version: 0.4.2-2 Installed-Size: 6373 Maintainer: Debian Med Packaging Team Architecture: all Description: convert various sequence formats to FASTA (example data) Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Description-md5: 0894149c7f5c7fc45635d76eaa073f5a Section: science Priority: optional Filename: pool/main/a/any2fasta/any2fasta-examples_0.4.2-2_all.deb Size: 6509616 MD5sum: cdeb2e2cb4504c336849593df46d5389 SHA256: 7345afc5878efe867285622415a0ba70b9c32bbd57849df63c4600217c4502f9 [sid] Package: any2fasta-examples Source: any2fasta Version: 0.4.2-2 Installed-Size: 6373 Maintainer: Debian Med Packaging Team Architecture: all Description: convert various sequence formats to FASTA (example data) Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Description-md5: 0894149c7f5c7fc45635d76eaa073f5a Section: science Priority: optional Filename: pool/main/a/any2fasta/any2fasta-examples_0.4.2-2_all.deb Size: 6509616 MD5sum: cdeb2e2cb4504c336849593df46d5389 SHA256: 7345afc5878efe867285622415a0ba70b9c32bbd57849df63c4600217c4502f9 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 any2fasta-examples=0.4.2-2 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 1.1.5 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 any2fasta-examples=0.4.2-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp9qpha97q 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp9qpha97q 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/proc'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/proc'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/ptmx'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/ptmx'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/console'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/console'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/shm'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/shm'] 0m2.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.5s DEBUG: Created resolv.conf. 0m2.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp9qpha97q/tmp/scripts/ 0m2.5s INFO: Running scripts post_chroot_unpack 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'update'] 0m5.5s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [164 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8872 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5989 kB] Fetched 15.0 MB in 2s (6705 kB/s) Reading package lists... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'update'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-yf', 'dist-upgrade'] 0m6.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: dash 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 91.8 kB of archives. After this operation, 23.6 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 91.8 kB in 0s (2449 kB/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 ... 8050 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-2_amd64.deb ... Unpacking dash (0.5.12-2) over (0.5.11+git20210903+057cd650a4ed-9) ... Setting up dash (0.5.12-2) ... Processing triggers for debianutils (5.7-0.4) ... 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-yf', 'dist-upgrade'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s DUMP: 407ed3f9753e8ab24ae5331b6eed0956 - 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s INFO: Running scripts post_setup 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s 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 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.3s 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' 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_zz_backports'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_setup_zz_backports'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DUMP: install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.81 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-3 install ok installed dpkg dpkg 1.21.13 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-13 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libattr1:amd64 libattr1 1:2.5.1-3 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-7 install ok installed libc6:amd64 libc6 2.36-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.266 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-13 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.0-0.1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-3 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b4 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b4 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-13 install ok installed libsystemd0:amd64 libsystemd0 252.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-1 install ok installed libudev1:amd64 libudev1 252.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg2-3 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.4-1 install ok installed ncurses-bin ncurses-bin 6.4-1 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-6 install ok installed perl-base perl-base 5.36.0-6 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-6 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.06-2 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022g-1 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m8.9s INFO: Running scripts is_testable 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s INFO: Running scripts pre_test 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_test_root_password'] 0m8.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_test_root_password'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'show', '--no-all-versions', 'any2fasta-examples'] 0m9.2s DUMP: Package: any2fasta-examples Source: any2fasta Version: 0.4.2-2 Installed-Size: 6373 Maintainer: Debian Med Packaging Team Architecture: all Description-en: convert various sequence formats to FASTA (example data) Established tools like readseq and seqret from EMBOSS, both create mangled IDs containing | or . characters, and there is no way to fix this behaviour. This resultes in inconsitences between .gbk and .fna versions of files in pipelines. . This script uses only core Perl modules, has no other dependencies like Bioperl or Biopython, and runs very quickly. . It supports the following input formats: . 1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS) 2. EMBL flat file, typically .embl, (starts with ID) 3. GFF with sequence, typically .gff, .gff3 (starts with ##gff) 4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >) 5. FASTQ DNA, typically .fastq, .fq (starts with @) 6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE) 7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM) 8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t) . Files may be compressed with: . 1. gzip, typically .gz 2. bzip2, typically .bz2 3. zip, typically .zip . This package contains some example data for testing. Description-md5: 0894149c7f5c7fc45635d76eaa073f5a Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Section: science Priority: optional Filename: pool/main/a/any2fasta/any2fasta-examples_0.4.2-2_all.deb Size: 6509616 MD5sum: cdeb2e2cb4504c336849593df46d5389 SHA256: 7345afc5878efe867285622415a0ba70b9c32bbd57849df63c4600217c4502f9 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'show', '--no-all-versions', 'any2fasta-examples'] 0m9.2s INFO: apt-cache knows about the following packages: any2fasta-examples 0m9.2s INFO: Running scripts pre_install 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m9.3s 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: 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m9.3s DUMP: any2fasta-examples: Installed: (none) Candidate: 0.4.2-2 Version table: 0.4.2-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples'] 0m10.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: any2fasta-examples 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 6510 kB of archives. After this operation, 6526 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 any2fasta-examples all 0.4.2-2 [6510 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6510 kB in 0s (55.5 MB/s) Selecting previously unselected package any2fasta-examples. (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 ... 8052 files and directories currently installed.) Preparing to unpack .../any2fasta-examples_0.4.2-2_all.deb ... Unpacking any2fasta-examples (0.4.2-2) ... Setting up any2fasta-examples (0.4.2-2) ... 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples'] 0m10.2s INFO: Running scripts post_install 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m10.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m10.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp9qpha97q to sid 0m10.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m10.6s INFO: Running scripts pre_distupgrade 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'update'] 0m15.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [161 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9402 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6952 kB] Fetched 16.5 MB in 4s (4161 kB/s) Reading package lists... 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'update'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-yf', 'dist-upgrade'] 0m21.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debconf dpkg findutils gcc-12-base libc-bin libc6 libcrypt1 libgcc-s1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libstdc++6 perl perl-base perl-modules-5.36 sed tar 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 17.3 MB of archives. After this operation, 1041 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.1 [836 kB] Get:2 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.21.17 [1503 kB] Get:3 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.36 amd64 5.36.0-7 [4218 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.36.0-7 [239 kB] Get:6 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.36.0-7 [1608 kB] Get:7 http://deb.debian.org/debian sid/main amd64 perl-modules-5.36 all 5.36.0-7 [2815 kB] Get:8 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.36-8 [2747 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:13 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-1 [329 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.36-8 [605 kB] Get:15 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.82 [121 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-6 [91.7 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-6 [75.5 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-6 [291 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-6 [161 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.3 MB in 0s (56.5 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.36-8) ... 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-yf', 'dist-upgrade'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m21.5s DUMP: 4c8c463dcb95f10e5d12cb144f90d7c2 - 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'show', '--no-all-versions', 'any2fasta-examples'] 0m21.7s DUMP: Package: any2fasta-examples Source: any2fasta Version: 0.4.2-2 Installed-Size: 6373 Maintainer: Debian Med Packaging Team Architecture: all Description-en: convert various sequence formats to FASTA (example data) Established tools like readseq and seqret from EMBOSS, both create mangled IDs containing | or . characters, and there is no way to fix this behaviour. This resultes in inconsitences between .gbk and .fna versions of files in pipelines. . This script uses only core Perl modules, has no other dependencies like Bioperl or Biopython, and runs very quickly. . It supports the following input formats: . 1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS) 2. EMBL flat file, typically .embl, (starts with ID) 3. GFF with sequence, typically .gff, .gff3 (starts with ##gff) 4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >) 5. FASTQ DNA, typically .fastq, .fq (starts with @) 6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE) 7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM) 8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t) . Files may be compressed with: . 1. gzip, typically .gz 2. bzip2, typically .bz2 3. zip, typically .zip . This package contains some example data for testing. Description-md5: 0894149c7f5c7fc45635d76eaa073f5a Multi-Arch: foreign Homepage: https://github.com/tseemann/any2fasta Section: science Priority: optional Filename: pool/main/a/any2fasta/any2fasta-examples_0.4.2-2_all.deb Size: 6509616 MD5sum: cdeb2e2cb4504c336849593df46d5389 SHA256: 7345afc5878efe867285622415a0ba70b9c32bbd57849df63c4600217c4502f9 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'show', '--no-all-versions', 'any2fasta-examples'] 0m21.7s INFO: apt-cache knows about the following packages: any2fasta-examples 0m21.7s INFO: Running scripts pre_install 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m21.8s 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: 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m21.9s DUMP: any2fasta-examples: Installed: 0.4.2-2 Candidate: 0.4.2-2 Version table: *** 0.4.2-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples'] 0m22.4s DUMP: Reading package lists... Building dependency tree... Reading state information... any2fasta-examples is already the newest version (0.4.2-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples'] 0m22.4s INFO: Running scripts post_install 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m22.4s INFO: Running scripts post_distupgrade 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m22.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m22.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m23.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m23.0s INFO: Running scripts pre_install 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_database-server'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_exceptions'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_extras'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m23.2s 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: 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m23.2s DUMP: any2fasta-examples: Installed: 0.4.2-2 Candidate: 0.4.2-2 Version table: *** 0.4.2-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-cache', 'policy', 'any2fasta-examples'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples=0.4.2-2'] 0m23.7s DUMP: Reading package lists... Building dependency tree... Reading state information... any2fasta-examples is already the newest version (0.4.2-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', '-y', 'install', 'any2fasta-examples=0.4.2-2'] 0m23.7s INFO: Running scripts post_install 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_install_exceptions'] 0m23.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m24.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m24.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', '-ac', '--ignore-obsolete'] 0m25.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', '-ac', '--ignore-obsolete'] 0m25.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m25.2s DUMP: 0.15.6 0m25.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m25.2s INFO: Running adequate version 0.15.6 now. 0m25.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'any2fasta-examples'] 0m25.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'any2fasta-examples'] 0m25.3s INFO: Running scripts pre_remove 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_exceptions'] 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/pre_remove_exceptions'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.9s DUMP: install ok installed any2fasta-examples any2fasta-examples 0.4.2-2 install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-3 install ok installed dpkg dpkg 1.21.17 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libattr1:amd64 libattr1 1:2.5.1-3 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-8 install ok installed libc6:amd64 libc6 2.36-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.266 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.0-0.1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b4 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b4 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-1 install ok installed libudev1:amd64 libudev1 252.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg2-3 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.4-1 install ok installed ncurses-bin ncurses-bin 6.4-1 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-2 install ok installed tar tar 1.34+dfsg-1.1 install ok installed tzdata tzdata 2022g-1 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'remove', 'any2fasta-examples'] 0m26.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: any2fasta-examples 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 6526 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 ... 8067 files and directories currently installed.) Removing any2fasta-examples (0.4.2-2) ... 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'remove', 'any2fasta-examples'] 0m26.8s INFO: Running scripts post_remove 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_remove_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_remove_exceptions'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--purge', 'any2fasta-examples'] 0m26.8s DUMP: dpkg: warning: ignoring request to remove any2fasta-examples which isn't installed 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--purge', 'any2fasta-examples'] 0m26.8s INFO: Running scripts post_purge 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_purge_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_purge_exceptions'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--purge', '--pending'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--purge', '--pending'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--remove', '--pending'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg', '--remove', '--pending'] 0m26.8s INFO: Running scripts post_test 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_test_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'tmp/scripts/post_test_exceptions'] 0m26.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m27.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-divert', '--list'] 0m27.3s 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 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'dpkg-divert', '--list'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'clean'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qpha97q', 'apt-get', 'clean'] 0m27.3s DEBUG: Recording chroot state 0m28.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/shm'] 0m28.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/shm'] 0m28.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/console'] 0m28.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/console'] 0m28.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/ptmx'] 0m28.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/ptmx'] 0m28.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts'] 0m28.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/dev/pts'] 0m28.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/proc'] 0m28.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qpha97q/proc'] 0m28.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m28.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9qpha97q'] 0m28.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp9qpha97q 0m28.4s INFO: PASS: Upgrading between Debian distributions. 0m28.4s INFO: PASS: All tests. 0m28.4s INFO: piuparts run ends. ret=0 End: 2023-01-10 15:54:54 GMT