Start: 2022-11-07 03:45:11 GMT [testing] Package: samclip Version: 0.4.0-3 Installed-Size: 172 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any Description: filter SAM file for soft and hard clipped alignments Multi-Arch: foreign Homepage: https://github.com/tseemann/samclip Description-md5: 05f5ccd9490c515b8a4bba32a37db5c8 Section: science Priority: optional Filename: pool/main/s/samclip/samclip_0.4.0-3_all.deb Size: 20068 MD5sum: 037cb4851d4547f0ba978fcc0df7f169 SHA256: 6624093005231d61a3a1d1c8b4bea88e2b02d5c3b0f6dcae2ad5e256e26e52f5 [sid] Package: samclip Version: 0.4.0-4 Installed-Size: 172 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any Description: filter SAM file for soft and hard clipped alignments Multi-Arch: foreign Homepage: https://github.com/tseemann/samclip Description-md5: 05f5ccd9490c515b8a4bba32a37db5c8 Section: science Priority: optional Filename: pool/main/s/samclip/samclip_0.4.0-4_all.deb Size: 20124 MD5sum: 51af01f6255128f952ef9d6fd7ff00d1 SHA256: d8d091bfab2ac3d3430fb7cecdc4162ba61f19bdc70f2e6df170bbce6e71e43b 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 samclip=0.4.0-4 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 samclip=0.4.0-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpv1mkj9ws 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpv1mkj9ws 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', '-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/tmpv1mkj9ws/proc'] 0m2.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/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/tmpv1mkj9ws/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/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/tmpv1mkj9ws/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'update'] 0m5.3s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [164 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8714 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5893 kB] Fetched 14.8 MB in 2s (6907 kB/s) Reading package lists... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'update'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-yf', 'dist-upgrade'] 0m7.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt grep libapt-pkg6.0 libpcre2-8-0 libsystemd0 libudev1 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3378 kB of archives. After this operation, 133 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-3 [421 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252-2 [327 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252-2 [105 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.5.4 [902 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.5.4 [1362 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.40-2 [260 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3378 kB in 0s (31.7 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 ... 8689 files and directories currently installed.) Preparing to unpack .../archives/grep_3.8-3_amd64.deb ... Unpacking grep (3.8-3) over (3.7-1) ... Setting up grep (3.8-3) ... (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 ... 8691 files and directories currently installed.) Preparing to unpack .../libsystemd0_252-2_amd64.deb ... Unpacking libsystemd0:amd64 (252-2) over (251.6-1) ... Setting up libsystemd0:amd64 (252-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8691 files and directories currently installed.) Preparing to unpack .../libudev1_252-2_amd64.deb ... Unpacking libudev1:amd64 (252-2) over (251.6-1) ... Setting up libudev1:amd64 (252-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8691 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.5.4_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.5.4) over (2.5.3+b1) ... Setting up libapt-pkg6.0:amd64 (2.5.4) ... (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 ... 8690 files and directories currently installed.) Preparing to unpack .../archives/apt_2.5.4_amd64.deb ... Unpacking apt (2.5.4) over (2.5.3+b1) ... Setting up apt (2.5.4) ... (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 ... 8689 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.40-2_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.40-2) over (10.40-1) ... Setting up libpcre2-8-0:amd64 (10.40-2) ... Processing triggers for libc-bin (2.35-4) ... 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-yf', 'dist-upgrade'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.3s DUMP: 4a22141728a5a47159c3413acd51693a - 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.3s INFO: Running scripts post_setup 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_dummy_users'] 0m8.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_dummy_users'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_forbid_home'] 0m8.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_forbid_home'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.9s 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' 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_minimize'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_minimize'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_zz_backports'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_setup_zz_backports'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.0s DUMP: install ok installed adduser adduser 3.129 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 5.2-2 install ok installed bsdutils bsdutils 1:2.38.1-1.1+b1 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+b1 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 12.2.0-3 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 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 2.5.4 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+b1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1.1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-4 install ok installed libc6:amd64 libc6 2.35-4 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+b1 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+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 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 1.23-3 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 3.7.8-2 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 5.2.7-0.1 install ok installed libmount1:amd64 libmount1 2.38.1-1.1+b1 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 0.24.1-1 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 10.40-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 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 2.38.1-1.1+b1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 252-2 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 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-1.1+b1 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 1:4.12.3+dfsg1-2 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 2.38.1-1.1+b1 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 1:4.12.3+dfsg1-2 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 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 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-1.1+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-1.1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m9.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m9.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m9.4s INFO: Running scripts is_testable 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/is_testable_uninstallable'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/is_testable_uninstallable'] 0m9.4s INFO: Running scripts pre_test 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_test_exceptions'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_test_exceptions'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_test_root_password'] 0m9.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_test_root_password'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'show', '--no-all-versions', 'samclip'] 0m9.6s DUMP: Package: samclip Version: 0.4.0-3 Installed-Size: 172 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any Description-en: filter SAM file for soft and hard clipped alignments Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in --end-to-end mode). This means the ends of the read may not be part of the best alignment. . This can be caused by: . * adapter sequences (aren't in the reference) * poor quality bases (mismatches only make the alignment score worse) * structural variation in your sample compared to the reference * reads overlapping the start and end of contigs (including circular genomes) . Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn't. The unaligned ends of the read can be "soft" or "hard" clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don't mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not. Description-md5: 05f5ccd9490c515b8a4bba32a37db5c8 Multi-Arch: foreign Homepage: https://github.com/tseemann/samclip Section: science Priority: optional Filename: pool/main/s/samclip/samclip_0.4.0-3_all.deb Size: 20068 MD5sum: 037cb4851d4547f0ba978fcc0df7f169 SHA256: 6624093005231d61a3a1d1c8b4bea88e2b02d5c3b0f6dcae2ad5e256e26e52f5 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'show', '--no-all-versions', 'samclip'] 0m9.6s INFO: apt-cache knows about the following packages: samclip 0m9.6s INFO: Running scripts pre_install 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m9.7s 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: 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m9.8s DUMP: samclip: Installed: (none) Candidate: 0.4.0-3 Version table: 0.4.0-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip'] 0m10.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: samclip 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 20.1 kB of archives. After this operation, 176 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 samclip all 0.4.0-3 [20.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.1 kB in 0s (690 kB/s) Selecting previously unselected package samclip. (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 ... 8691 files and directories currently installed.) Preparing to unpack .../samclip_0.4.0-3_all.deb ... Unpacking samclip (0.4.0-3) ... Setting up samclip (0.4.0-3) ... 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip'] 0m10.5s INFO: Running scripts post_install 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m10.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m10.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpv1mkj9ws to sid 0m10.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m10.9s INFO: Running scripts pre_distupgrade 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'update'] 0m14.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [161 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9389 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6939 kB] Fetched 16.5 MB in 3s (5510 kB/s) Reading package lists... 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'update'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-yf', 'dist-upgrade'] 0m18.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bash debianutils gcc-12-base libc-bin libc6 libcrypt1 libgcc-s1 libgnutls30 libgpg-error0 libstdc++6 libsystemd0 libudev1 login passwd samclip zlib1g 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9316 kB of archives. After this operation, 485 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.36-4 [2747 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.36-4 [604 kB] Get:3 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.2.0-9 [37.0 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 12.2.0-9 [49.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 12.2.0-9 [614 kB] Get:6 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.7-0.4 [102 kB] Get:7 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2-2+b1 [1490 kB] Get:8 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.12.3+dfsg1-3 [606 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.30-1 [89.0 kB] Get:10 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.12.3+dfsg1-3 [972 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.7.8-4 [1389 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 252-3 [328 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 252-3 [106 kB] Get:15 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:16 http://deb.debian.org/debian sid/main amd64 samclip all 0.4.0-4 [20.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9316 kB in 0s (54.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8703 files and directories currently installed.) Preparing to unpack .../libc6_2.36-4_amd64.deb ... Unpacking libc6:amd64 (2.36-4) over (2.35-4) ... Setting up libc6:amd64 (2.36-4) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-4_amd64.deb ... Unpacking libc-bin (2.36-4) over (2.35-4) ... Setting up libc-bin (2.36-4) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../gcc-12-base_12.2.0-9_amd64.deb ... Unpacking gcc-12-base:amd64 (12.2.0-9) over (12.2.0-3) ... Setting up gcc-12-base:amd64 (12.2.0-9) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12.2.0-9_amd64.deb ... Unpacking libgcc-s1:amd64 (12.2.0-9) over (12.2.0-3) ... Setting up libgcc-s1:amd64 (12.2.0-9) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../libstdc++6_12.2.0-9_amd64.deb ... Unpacking libstdc++6:amd64 (12.2.0-9) over (12.2.0-3) ... Setting up libstdc++6:amd64 (12.2.0-9) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../debianutils_5.7-0.4_amd64.deb ... Unpacking debianutils (5.7-0.4) over (5.7-0.3) ... Setting up debianutils (5.7-0.4) ... (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 ... 8703 files and directories currently installed.) Preparing to unpack .../bash_5.2-2+b1_amd64.deb ... Unpacking bash (5.2-2+b1) over (5.2-2) ... Setting up bash (5.2-2+b1) ... 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 ... 8704 files and directories currently installed.) Preparing to unpack .../login_1%3a4.12.3+dfsg1-3_amd64.deb ... Unpacking login (1:4.12.3+dfsg1-3) over (1:4.12.3+dfsg1-2) ... Setting up login (1:4.12.3+dfsg1-3) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.30-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.30-1) over (1:4.4.28-2) ... Setting up libcrypt1:amd64 (1:4.4.30-1) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.12.3+dfsg1-3_amd64.deb ... Unpacking passwd (1:4.12.3+dfsg1-3) over (1:4.12.3+dfsg1-2) ... Setting up passwd (1:4.12.3+dfsg1-3) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.8-4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.8-4) over (3.7.8-2) ... Setting up libgnutls30:amd64 (3.7.8-4) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.46-1_amd64.deb ... Unpacking libgpg-error0:amd64 (1.46-1) over (1.45-2) ... Setting up libgpg-error0:amd64 (1.46-1) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../libsystemd0_252-3_amd64.deb ... Unpacking libsystemd0:amd64 (252-3) over (252-2) ... Setting up libsystemd0:amd64 (252-3) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../libudev1_252-3_amd64.deb ... Unpacking libudev1:amd64 (252-3) over (252-2) ... Setting up libudev1:amd64 (252-3) ... (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 ... 8704 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-4.1) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-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 ... 8704 files and directories currently installed.) Preparing to unpack .../samclip_0.4.0-4_all.deb ... Unpacking samclip (0.4.0-4) over (0.4.0-3) ... Setting up samclip (0.4.0-4) ... Processing triggers for libc-bin (2.36-4) ... Processing triggers for debianutils (5.7-0.4) ... 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-yf', 'dist-upgrade'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.9s DUMP: 4ab6fcca43d970342686c8bbeb7a82eb - 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'show', '--no-all-versions', 'samclip'] 0m19.1s DUMP: Package: samclip Version: 0.4.0-4 Installed-Size: 172 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any Description-en: filter SAM file for soft and hard clipped alignments Most short read aligners perform local alignment of reads to the reference genome. Examples includes bwa mem, minimap2, and bowtie2 (unless in --end-to-end mode). This means the ends of the read may not be part of the best alignment. . This can be caused by: . * adapter sequences (aren't in the reference) * poor quality bases (mismatches only make the alignment score worse) * structural variation in your sample compared to the reference * reads overlapping the start and end of contigs (including circular genomes) . Read aligners output a SAM file. Column 6 in this format stores the CIGAR string. which describes which parts of the read aligned and which didn't. The unaligned ends of the read can be "soft" or "hard" clipped, denoted with S and H at each end of the CIGAR string. It is possible for both types to be present, but that is not common. Soft and hard don't mean anything biologically, they just refer to whether the full read sequence is in the SAM file or not. Description-md5: 05f5ccd9490c515b8a4bba32a37db5c8 Multi-Arch: foreign Homepage: https://github.com/tseemann/samclip Section: science Priority: optional Filename: pool/main/s/samclip/samclip_0.4.0-4_all.deb Size: 20124 MD5sum: 51af01f6255128f952ef9d6fd7ff00d1 SHA256: d8d091bfab2ac3d3430fb7cecdc4162ba61f19bdc70f2e6df170bbce6e71e43b 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'show', '--no-all-versions', 'samclip'] 0m19.1s INFO: apt-cache knows about the following packages: samclip 0m19.1s INFO: Running scripts pre_install 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m19.2s 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: 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m19.2s DUMP: samclip: Installed: 0.4.0-4 Candidate: 0.4.0-4 Version table: *** 0.4.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip'] 0m19.7s DUMP: Reading package lists... Building dependency tree... Reading state information... samclip is already the newest version (0.4.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip'] 0m19.7s INFO: Running scripts post_install 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m19.7s INFO: Running scripts post_distupgrade 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m20.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m20.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m20.5s INFO: Running scripts pre_install 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_database-server'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_exceptions'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_extras'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m20.6s 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: 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m20.7s DUMP: samclip: Installed: 0.4.0-4 Candidate: 0.4.0-4 Version table: *** 0.4.0-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-cache', 'policy', 'samclip'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip=0.4.0-4'] 0m21.4s DUMP: Reading package lists... Building dependency tree... Reading state information... samclip is already the newest version (0.4.0-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', '-y', 'install', 'samclip=0.4.0-4'] 0m21.4s INFO: Running scripts post_install 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_install_exceptions'] 0m21.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m21.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m22.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', '-ac', '--ignore-obsolete'] 0m22.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', '-ac', '--ignore-obsolete'] 0m22.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.0s DUMP: 0.15.6 0m23.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.0s INFO: Running adequate version 0.15.6 now. 0m23.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'samclip'] 0m23.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'samclip'] 0m23.1s INFO: Running scripts pre_remove 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_exceptions'] 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/pre_remove_exceptions'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.8s DUMP: install ok installed adduser adduser 3.129 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 5.2-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-1.1+b1 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 5.7-0.4 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9+b1 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 12.2.0-9 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 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 2.5.4 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+b1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1.1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-4 install ok installed libc6:amd64 libc6 2.36-4 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+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.30-1 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 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 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 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 5.2.7-0.1 install ok installed libmount1:amd64 libmount1 2.38.1-1.1+b1 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 0.24.1-1 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 10.40-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 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 2.38.1-1.1+b1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 252-3 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 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-1.1+b1 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 1:4.12.3+dfsg1-3 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 2.38.1-1.1+b1 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 1:4.12.3+dfsg1-3 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed samclip samclip 0.4.0-4 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 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-1.1+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-1.1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'remove', 'samclip'] 0m24.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: samclip 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 176 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 ... 8704 files and directories currently installed.) Removing samclip (0.4.0-4) ... 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'remove', 'samclip'] 0m24.6s INFO: Running scripts post_remove 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_remove_exceptions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--purge', 'samclip'] 0m24.6s DUMP: dpkg: warning: ignoring request to remove samclip which isn't installed 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--purge', 'samclip'] 0m24.6s INFO: Running scripts post_purge 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_purge_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_purge_exceptions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--purge', '--pending'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--purge', '--pending'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--remove', '--pending'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg', '--remove', '--pending'] 0m24.6s INFO: Running scripts post_test 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_test_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'tmp/scripts/post_test_exceptions'] 0m24.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m24.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-divert', '--list'] 0m24.9s 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 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'dpkg-divert', '--list'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'clean'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws', 'apt-get', 'clean'] 0m24.9s DEBUG: Recording chroot state 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/shm'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/shm'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/console'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/console'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/ptmx'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/ptmx'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/pts'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/dev/pts'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/proc'] 0m25.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws/proc'] 0m25.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m26.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv1mkj9ws'] 0m26.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpv1mkj9ws 0m26.0s INFO: PASS: Upgrading between Debian distributions. 0m26.0s INFO: PASS: All tests. 0m26.0s INFO: piuparts run ends. ret=0 End: 2022-11-07 03:45:37 GMT