Start: 2022-09-30 09:45:42 GMT [testing] Package: bamclipper Version: 1.0.0-2 Installed-Size: 29 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, samtools, parallel Description: Remove gene-specific primer sequences from SAM/BAM alignments Homepage: https://github.com/tommyau/bamclipper Description-md5: 7d5dd073cc04ca30be12a4a982bfa1e6 Section: science Priority: optional Filename: pool/main/b/bamclipper/bamclipper_1.0.0-2_all.deb Size: 6120 MD5sum: c9dab39291d3d48136e90039c0f16ef7 SHA256: 3bd1b5c4903b2363d3c4c069a8453bae456c92769b8bbc5ab6a6325e59bce96d [sid] Package: bamclipper Version: 1.0.0-3 Installed-Size: 30 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, samtools, parallel Description: Remove gene-specific primer sequences from SAM/BAM alignments Homepage: https://github.com/tommyau/bamclipper Description-md5: 7d5dd073cc04ca30be12a4a982bfa1e6 Section: science Priority: optional Filename: pool/main/b/bamclipper/bamclipper_1.0.0-3_all.deb Size: 6436 MD5sum: 18ebbdc3942f00ea66fcd459138b08b2 SHA256: b718277d9a48679cd796affea29648d33d69154563f734c09d765784910b8146 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 bamclipper=1.0.0-3 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 bamclipper=1.0.0-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmps2f9s0cs 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmps2f9s0cs 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '-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/tmps2f9s0cs/proc'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/proc'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts'] 0m2.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/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. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmps2f9s0cs/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'update'] 0m5.2s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [161 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8491 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5781 kB] Fetched 14.4 MB in 2s (6454 kB/s) Reading package lists... 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'update'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3763 kB of archives. After this operation, 636 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.35-1 [2941 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.35-1 [822 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3763 kB in 0s (58.4 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 ... 8606 files and directories currently installed.) Preparing to unpack .../libc6_2.35-1_amd64.deb ... Unpacking libc6:amd64 (2.35-1) over (2.34-8) ... Setting up libc6:amd64 (2.35-1) ... (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 ... 8605 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-1_amd64.deb ... Unpacking libc-bin (2.35-1) over (2.34-8) ... Setting up libc-bin (2.35-1) ... 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s DUMP: 91cf7c352727da78bef8ca38e275ba07 - 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.3s INFO: Running scripts post_setup 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s DUMP: useradd warning: dummy100's uid 100 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '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/tmps2f9s0cs', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_minimize'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.2 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2~rc2-2 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed coreutils coreutils 8.32-4.1+b1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 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 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.2 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 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 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 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 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022c-1 install ok installed usr-is-merged usr-is-merged 31 install ok installed usrmerge usrmerge 31 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m8.9s INFO: Running scripts is_testable 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s INFO: Running scripts pre_test 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_test_root_password'] 0m9.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_test_root_password'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'show', '--no-all-versions', 'bamclipper'] 0m9.2s DUMP: Package: bamclipper Version: 1.0.0-2 Installed-Size: 29 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, samtools, parallel Description-en: Remove gene-specific primer sequences from SAM/BAM alignments Remove gene-specific primer sequences from SAM/BAM alignments of PCR amplicons by soft-clipping. . bamclipper.sh soft-clips gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Description-md5: 7d5dd073cc04ca30be12a4a982bfa1e6 Homepage: https://github.com/tommyau/bamclipper Section: science Priority: optional Filename: pool/main/b/bamclipper/bamclipper_1.0.0-2_all.deb Size: 6120 MD5sum: c9dab39291d3d48136e90039c0f16ef7 SHA256: 3bd1b5c4903b2363d3c4c069a8453bae456c92769b8bbc5ab6a6325e59bce96d 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'show', '--no-all-versions', 'bamclipper'] 0m9.2s INFO: apt-cache knows about the following packages: bamclipper 0m9.2s INFO: Running scripts pre_install 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '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/tmps2f9s0cs', 'apt-cache', 'policy'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m9.4s DUMP: bamclipper: Installed: (none) Candidate: 1.0.0-2 Version table: 1.0.0-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper'] 0m13.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libbrotli1 libcurl3-gnutls libdeflate0 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libncurses6 libncursesw6 libnghttp2-14 libprocps8 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh2-1 libssl3 parallel procps samtools sensible-utils sysstat ucf xz-utils Suggested packages: krb5-doc krb5-user lm-sensors ash csh fish ksh tcsh zsh cwltool isag Recommended packages: ca-certificates krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules psmisc systemd | cron | cron-daemon The following NEW packages will be installed: bamclipper libbrotli1 libcurl3-gnutls libdeflate0 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libncurses6 libncursesw6 libnghttp2-14 libprocps8 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh2-1 libssl3 parallel procps samtools sensible-utils sysstat ucf xz-utils 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 8867 kB of archives. After this operation, 22.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libprocps8 amd64 2:3.3.17-7+b1 [64.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:3.3.17-7+b1 [502 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043 [74.0 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 xz-utils amd64 5.2.5-2.1 [220 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b4 [275 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20-1 [65.7 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20-1 [111 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.5-2 [2030 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20-1 [363 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20-1 [166 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-8 [38.7 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-8 [78.2 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-1 [230 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.50.0-1 [76.1 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.85.0-1 [361 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.12-1 [71.6 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.2.2-1 [54.1 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.13+ds-2+b1 [397 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.13-4+b1 [577 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 sysstat amd64 12.5.6-1 [605 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 parallel all 20220722+ds-1 [1849 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 bamclipper all 1.0.0-2 [6120 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 8867 kB in 0s (22.2 MB/s) Selecting previously unselected package libncurses6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8606 files and directories currently installed.) Preparing to unpack .../00-libncurses6_6.3+20220423-2_amd64.deb ... Unpacking libncurses6:amd64 (6.3+20220423-2) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../01-libncursesw6_6.3+20220423-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.3+20220423-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../02-libprocps8_2%3a3.3.17-7+b1_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-7+b1) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a3.3.17-7+b1_amd64.deb ... Unpacking procps (2:3.3.17-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package xz-utils. Preparing to unpack .../06-xz-utils_5.2.5-2.1_amd64.deb ... Unpacking xz-utils (5.2.5-2.1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../07-libbrotli1_1.0.9-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../08-libkrb5support0_1.20-1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../09-libk5crypto3_1.20-1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../10-libkeyutils1_1.6.3-1_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../11-libssl3_3.0.5-2_amd64.deb ... Unpacking libssl3:amd64 (3.0.5-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../12-libkrb5-3_1.20-1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20-1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../13-libgssapi-krb5-2_1.20-1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../14-libsasl2-modules-db_2.1.28+dfsg-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../15-libsasl2-2_2.1.28+dfsg-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../16-libldap-2.5-0_2.5.13+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../17-libnghttp2-14_1.50.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.50.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../18-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../19-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../20-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../21-libcurl3-gnutls_7.85.0-1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.85.0-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../22-libdeflate0_1.12-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.12-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../23-libhtscodecs2_1.2.2-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.2.2-1) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../24-libhts3_1.13+ds-2+b1_amd64.deb ... Unpacking libhts3:amd64 (1.13+ds-2+b1) ... Selecting previously unselected package samtools. Preparing to unpack .../25-samtools_1.13-4+b1_amd64.deb ... Unpacking samtools (1.13-4+b1) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../26-libsensors-config_1%3a3.6.0-7_all.deb ... Unpacking libsensors-config (1:3.6.0-7) ... Selecting previously unselected package libsensors5:amd64. Preparing to unpack .../27-libsensors5_1%3a3.6.0-7_amd64.deb ... Unpacking libsensors5:amd64 (1:3.6.0-7) ... Selecting previously unselected package sysstat. Preparing to unpack .../28-sysstat_12.5.6-1_amd64.deb ... Unpacking sysstat (12.5.6-1) ... Selecting previously unselected package parallel. Preparing to unpack .../29-parallel_20220722+ds-1_all.deb ... Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20220722+ds-1) ... Selecting previously unselected package bamclipper. Preparing to unpack .../30-bamclipper_1.0.0-2_all.deb ... Unpacking bamclipper (1.0.0-2) ... Setting up libhtscodecs2:amd64 (1.2.2-1) ... Setting up libkeyutils1:amd64 (1.6.3-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libbrotli1:amd64 (1.0.9-2+b4) ... Setting up libssl3:amd64 (3.0.5-2) ... Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:amd64 (1.50.0-1) ... Setting up libdeflate0:amd64 (1.12-1) ... Setting up libkrb5support0:amd64 (1.20-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-8) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.3+20220423-2) ... Setting up xz-utils (5.2.5-2.1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libk5crypto3:amd64 (1.20-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-8) ... Setting up sensible-utils (0.0.17) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20-1) ... Setting up libprocps8:amd64 (2:3.3.17-7+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.20-1) ... Setting up ucf (3.0043) ... Setting up procps (2:3.3.17-7+b1) ... Setting up sysstat (12.5.6-1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libcurl3-gnutls:amd64 (7.85.0-1) ... Setting up parallel (20220722+ds-1) ... Setting up libhts3:amd64 (1.13+ds-2+b1) ... Setting up samtools (1.13-4+b1) ... Setting up bamclipper (1.0.0-2) ... Processing triggers for libc-bin (2.35-1) ... 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper'] 0m13.3s INFO: Running scripts post_install 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m13.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m13.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m13.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmps2f9s0cs to sid 0m13.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m13.7s INFO: Running scripts pre_distupgrade 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'update'] 0m17.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [158 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9349 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6912 kB] Fetched 16.4 MB in 3s (5369 kB/s) Reading package lists... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'update'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-yf', 'dist-upgrade'] 0m21.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bamclipper bash coreutils grep libapt-pkg6.0 libffi8 libhtscodecs2 libldap-2.5-0 libssl3 tzdata usr-is-merged usrmerge 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 10.1 MB of archives. After this operation, 860 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2-1 [1524 kB] Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:3 http://deb.debian.org/debian sid/main amd64 grep amd64 3.8-2 [432 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.5.3 [1044 kB] Get:5 http://deb.debian.org/debian sid/main amd64 apt amd64 2.5.3 [1505 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.3-2 [26.1 kB] Get:7 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 32 [5524 B] Get:8 http://deb.debian.org/debian sid/main amd64 usrmerge all 32 [13.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 tzdata all 2022d-1 [290 kB] Get:10 http://deb.debian.org/debian sid/main amd64 bamclipper all 1.0.0-3 [6436 B] Get:11 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.3.0-2 [87.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-2 [230 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.5-4 [2031 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.1 MB in 0s (79.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9335 files and directories currently installed.) Preparing to unpack .../archives/bash_5.2-1_amd64.deb ... Unpacking bash (5.2-1) over (5.2~rc2-2) ... Setting up bash (5.2-1) ... 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 ... 9335 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1_amd64.deb ... Unpacking coreutils (9.1-1) over (8.32-4.1+b1) ... Setting up coreutils (9.1-1) ... (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 ... 9336 files and directories currently installed.) Preparing to unpack .../usr-is-merged_32_all.deb ... W: /etc/unsupported-skip-usrmerge-conversion exists. Unpacking usr-is-merged (32) over (31) ... Setting up usr-is-merged (32) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9336 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_32_all.deb ... Unpacking usrmerge (32) over (31) ... Setting up usrmerge (32) ... W: /etc/unsupported-skip-usrmerge-conversion exists. (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 ... 9336 files and directories currently installed.) Preparing to unpack .../tzdata_2022d-1_all.deb ... Unpacking tzdata (2022d-1) over (2022c-1) ... Preparing to unpack .../bamclipper_1.0.0-3_all.deb ... Unpacking bamclipper (1.0.0-3) over (1.0.0-2) ... Preparing to unpack .../libhtscodecs2_1.3.0-2_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-2) over (1.2.2-1) ... Preparing to unpack .../libldap-2.5-0_2.5.13+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-2) over (2.5.13+dfsg-1) ... Preparing to unpack .../libssl3_3.0.5-4_amd64.deb ... Unpacking libssl3:amd64 (3.0.5-4) over (3.0.5-2) ... Setting up libhtscodecs2:amd64 (1.3.0-2) ... Setting up bamclipper (1.0.0-3) ... Setting up libssl3:amd64 (3.0.5-4) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-2) ... Setting up tzdata (2022d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 30 09:46:03 UTC 2022. Universal Time is now: Fri Sep 30 09:46:03 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.35-1) ... Processing triggers for debianutils (5.7-0.3) ... 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-yf', 'dist-upgrade'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.6s DUMP: 1ea7785b9be1b0f9c55de473966c018f - 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'show', '--no-all-versions', 'bamclipper'] 0m22.9s DUMP: Package: bamclipper Version: 1.0.0-3 Installed-Size: 30 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, samtools, parallel Description-en: Remove gene-specific primer sequences from SAM/BAM alignments Remove gene-specific primer sequences from SAM/BAM alignments of PCR amplicons by soft-clipping. . bamclipper.sh soft-clips gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. Description-md5: 7d5dd073cc04ca30be12a4a982bfa1e6 Homepage: https://github.com/tommyau/bamclipper Section: science Priority: optional Filename: pool/main/b/bamclipper/bamclipper_1.0.0-3_all.deb Size: 6436 MD5sum: 18ebbdc3942f00ea66fcd459138b08b2 SHA256: b718277d9a48679cd796affea29648d33d69154563f734c09d765784910b8146 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'show', '--no-all-versions', 'bamclipper'] 0m22.9s INFO: apt-cache knows about the following packages: bamclipper 0m22.9s INFO: Running scripts pre_install 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '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/tmps2f9s0cs', 'apt-cache', 'policy'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m23.0s DUMP: bamclipper: Installed: 1.0.0-3 Candidate: 1.0.0-3 Version table: *** 1.0.0-3 500 500 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/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper'] 0m23.5s DUMP: Reading package lists... Building dependency tree... Reading state information... bamclipper is already the newest version (1.0.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper'] 0m23.5s INFO: Running scripts post_install 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m23.5s INFO: Running scripts post_distupgrade 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m23.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m23.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m24.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m24.2s INFO: Running scripts pre_install 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_database-server'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_exceptions'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_extras'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy'] 0m24.3s 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: 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m24.3s DUMP: bamclipper: Installed: 1.0.0-3 Candidate: 1.0.0-3 Version table: *** 1.0.0-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-cache', 'policy', 'bamclipper'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper=1.0.0-3'] 0m24.8s DUMP: Reading package lists... Building dependency tree... Reading state information... bamclipper is already the newest version (1.0.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', '-y', 'install', 'bamclipper=1.0.0-3'] 0m24.8s INFO: Running scripts post_install 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_install_exceptions'] 0m24.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m25.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m25.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '-ac', '--ignore-obsolete'] 0m26.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', '-ac', '--ignore-obsolete'] 0m26.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.8s DUMP: 0.15.6 0m26.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.8s INFO: Running adequate version 0.15.6 now. 0m26.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'bamclipper'] 0m26.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'bamclipper'] 0m26.9s INFO: Running scripts pre_remove 0m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_exceptions'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/pre_remove_exceptions'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.0s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.3 install ok installed bamclipper bamclipper 1.0.0-3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-1 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 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 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.8-2 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 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 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.85.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libdeflate0:amd64 libdeflate0 1.12-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.3-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.13+ds-2+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20-1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-1 install ok installed libkrb5-3:amd64 libkrb5-3 1.20-1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20-1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libncurses6:amd64 libncurses6 6.3+20220423-2 install ok installed libncursesw6:amd64 libncursesw6 6.3+20220423-2 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.50.0-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-7+b1 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-7 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.5-4 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed parallel parallel 20220722+ds-1 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed procps procps 2:3.3.17-7+b1 install ok installed samtools samtools 1.13-4+b1 install ok installed sed sed 4.8-1 install ok installed sensible-utils sensible-utils 0.0.17 install ok installed sysstat sysstat 12.5.6-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022d-1 install ok installed ucf ucf 3.0043 install ok installed usr-is-merged usr-is-merged 32 install ok installed usrmerge usrmerge 32 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed xz-utils xz-utils 5.2.5-2.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'remove', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'parallel', 'procps', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'xz-utils', 'bamclipper'] 0m28.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bamclipper libbrotli1 libcurl3-gnutls libdeflate0 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libncurses6 libncursesw6 libnghttp2-14 libprocps8 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libssh2-1 libssl3 parallel procps samtools sensible-utils sysstat ucf xz-utils 0 upgraded, 0 newly installed, 31 to remove and 0 not upgraded. After this operation, 22.7 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9337 files and directories currently installed.) Removing bamclipper (1.0.0-3) ... Removing samtools (1.13-4+b1) ... Removing libhts3:amd64 (1.13+ds-2+b1) ... Removing libcurl3-gnutls:amd64 (7.85.0-1) ... Removing libbrotli1:amd64 (1.0.9-2+b4) ... Removing libdeflate0:amd64 (1.12-1) ... Removing libgssapi-krb5-2:amd64 (1.20-1) ... Removing libhtscodecs2:amd64 (1.3.0-2) ... Removing libkrb5-3:amd64 (1.20-1) ... Removing libk5crypto3:amd64 (1.20-1) ... Removing libkeyutils1:amd64 (1.6.3-1) ... Removing libkrb5support0:amd64 (1.20-1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-2) ... Removing parallel (20220722+ds-1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing procps (2:3.3.17-7+b1) ... Removing libncurses6:amd64 (6.3+20220423-2) ... Removing libncursesw6:amd64 (6.3+20220423-2) ... Removing libnghttp2-14:amd64 (1.50.0-1) ... Removing libprocps8:amd64 (2:3.3.17-7+b1) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-8) ... Removing sysstat (12.5.6-1) ... Removing libsensors5:amd64 (1:3.6.0-7) ... Removing libsensors-config (1:3.6.0-7) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing libssl3:amd64 (3.0.5-4) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.17) ... Removing xz-utils (5.2.5-2.1) ... Processing triggers for libc-bin (2.35-1) ... 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'remove', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'parallel', 'procps', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'xz-utils', 'bamclipper'] 0m28.8s INFO: Running scripts post_remove 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_remove_exceptions'] 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_remove_exceptions'] 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'parallel', 'procps', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'xz-utils'] 0m29.3s DUMP: dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed (Reading database ... 8622 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20-1) ... dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-7) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed Purging configuration files for parallel (20220722+ds-1) ... Purging configuration files for procps (2:3.3.17-7+b1) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sysstat (12.5.6-1) ... Purging configuration files for ucf (3.0043) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'parallel', 'procps', 'samtools', 'sensible-utils', 'sysstat', 'ucf', 'xz-utils'] 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', 'bamclipper'] 0m29.3s DUMP: dpkg: warning: ignoring request to remove bamclipper which isn't installed 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', 'bamclipper'] 0m29.3s INFO: Running scripts post_purge 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_purge_exceptions'] 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_purge_exceptions'] 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', '--pending'] 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--purge', '--pending'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--remove', '--pending'] 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg', '--remove', '--pending'] 0m29.4s INFO: Running scripts post_test 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_test_exceptions'] 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'tmp/scripts/post_test_exceptions'] 0m29.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m29.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-divert', '--list'] 0m29.8s 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 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'dpkg-divert', '--list'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'clean'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs', 'apt-get', 'clean'] 0m29.8s DEBUG: Recording chroot state 0m30.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/shm'] 0m30.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/shm'] 0m30.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/console'] 0m30.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/console'] 0m30.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/ptmx'] 0m30.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/ptmx'] 0m30.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts'] 0m30.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/dev/pts'] 0m30.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/proc'] 0m30.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs/proc'] 0m30.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m30.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps2f9s0cs'] 0m30.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmps2f9s0cs 0m30.9s INFO: PASS: Upgrading between Debian distributions. 0m30.9s INFO: PASS: All tests. 0m30.9s INFO: piuparts run ends. ret=0 End: 2022-09-30 09:46:13 GMT