Start: 2026-09-04 10:20:28 GMT [testing] Package: atropos Source: atropos (1.1.32+dfsg-2) Version: 1.1.32+dfsg-2+b3 Installed-Size: 1279 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), python3 (<< 3.15), python3 (>= 3.13~), python3:any, python3-pysam Recommends: python3-jinja2 Description: NGS read trimming tool that is specific, sensitive, and speedy Homepage: https://github.com/jdidion/atropos Description-md5: 6d8a51e28a71effebfff42f9cbd1e5bc Section: science Priority: optional Filename: pool/main/a/atropos/atropos_1.1.32+dfsg-2+b3_amd64.deb Size: 265400 MD5sum: d23597f5ddefa7b15c46675d948b8840 SHA256: 6ae34676dcc1712eb4844fb9d8ccf0af1b58f53b2ebe89756f92a96a9261496e [sid] Package: atropos Source: atropos (1.1.32+dfsg-2) Version: 1.1.32+dfsg-2+b4 Installed-Size: 923 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), python3 (<< 3.15), python3 (>= 3.14~), python3:any, python3-pysam Recommends: python3-jinja2 Description: NGS read trimming tool that is specific, sensitive, and speedy Homepage: https://github.com/jdidion/atropos Description-md5: 6d8a51e28a71effebfff42f9cbd1e5bc Section: science Priority: optional Filename: pool/main/a/atropos/atropos_1.1.32+dfsg-2+b4_amd64.deb Size: 221116 MD5sum: 8590d4c6098a42ed4e8db9de09aa52b2 SHA256: f3edd3fe5422eb11573133ddfad1a9772048665011438123f8970e2d25bcbc13 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt atropos=1.1.32+dfsg-2+b4 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 1.6.1~202608291513~1.6.0-23-g1172a6e5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt atropos=1.1.32+dfsg-2+b4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.12.107+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.107-1 (2026-08-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpepgie0sc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpepgie0sc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/14', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/14', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpepgie0sc/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'update'] 0m2.1s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [151 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9924 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6573 kB] Fetched 16.6 MB in 1s (15.6 MB/s) Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-yf', 'dist-upgrade'] 0m4.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bsdutils debianutils libblkid1 libc-bin libc-gconv-modules-extra libc6 libmount1 libsmartcols1 libuuid1 login mount util-linux 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5908 kB of archives. After this operation, 175 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 debianutils amd64 5.24 [93.3 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libc-gconv-modules-extra amd64 2.43-4 [1101 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libc6 amd64 2.43-4 [1866 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.42.2-4 [34.4 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.42.2-4 [185 kB] Get:6 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.42.2-4 [230 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.42.2-4 [153 kB] Get:8 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.42.2-4 [1244 kB] Get:9 http://deb.debian.org/debian forky/main amd64 mount amd64 2.42.2-4 [169 kB] Get:10 http://deb.debian.org/debian forky/main amd64 libc-bin amd64 2.43-4 [620 kB] Get:11 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.42.2-4 [121 kB] Get:12 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.42.2-4 [92.9 kB] Preconfiguring packages ... Fetched 5908 kB in 0s (60.5 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 ... 4976 files and directories currently installed.) Preparing to unpack .../debianutils_5.24_amd64.deb ... Unpacking debianutils (5.24) over (5.23.2) ... Setting up debianutils (5.24) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libc-gconv-modules-extra_2.43-4_amd64.deb ... Unpacking libc-gconv-modules-extra:amd64 (2.43-4) over (2.43-3) ... Setting up libc-gconv-modules-extra:amd64 (2.43-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libc6_2.43-4_amd64.deb ... Unpacking libc6:amd64 (2.43-4) over (2.43-3) ... Setting up libc6:amd64 (2.43-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libuuid1_2.42.2-4_amd64.deb ... Unpacking libuuid1:amd64 (2.42.2-4) over (2.42.2-2) ... Setting up libuuid1:amd64 (2.42.2-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libblkid1_2.42.2-4_amd64.deb ... Unpacking libblkid1:amd64 (2.42.2-4) over (2.42.2-2) ... Setting up libblkid1:amd64 (2.42.2-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libmount1_2.42.2-4_amd64.deb ... Unpacking libmount1:amd64 (2.42.2-4) over (2.42.2-2) ... Setting up libmount1:amd64 (2.42.2-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.42.2-4_amd64.deb ... Unpacking libsmartcols1:amd64 (2.42.2-4) over (2.42.2-2) ... Setting up libsmartcols1:amd64 (2.42.2-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../util-linux_2.42.2-4_amd64.deb ... Unpacking util-linux (2.42.2-4) over (2.42.2-2) ... Setting up util-linux (2.42.2-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../mount_2.42.2-4_amd64.deb ... Unpacking mount (2.42.2-4) over (2.42.2-2) ... Preparing to unpack .../libc-bin_2.43-4_amd64.deb ... Unpacking libc-bin (2.43-4) over (2.43-3) ... Setting up libc-bin (2.43-4) ... (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 ... 4976 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.42.2-4_amd64.deb ... Unpacking login (1:4.16.0-2+really2.42.2-4) over (1:4.16.0-2+really2.42.2-2) ... Preparing to unpack .../bsdutils_1%3a2.42.2-4_amd64.deb ... Unpacking bsdutils (1:2.42.2-4) over (1:2.42.2-2) ... Setting up bsdutils (1:2.42.2-4) ... Setting up mount (2.42.2-4) ... Setting up login (1:4.16.0-2+really2.42.2-4) ... 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-yf', 'dist-upgrade'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.0s DUMP: 6e313a78f0271e37feb01ad34f8a292c - 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.0s INFO: Running scripts post_setup 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s 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 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DUMP: install ok installed apt apt 3.3.3 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-3+b1 install ok installed bsdutils bsdutils 1:2.42.2-4 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.7 install ok installed findutils findutils 4.11.0-2 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-1 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu1 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.3 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b1 install ok installed libblkid1:amd64 libblkid1 2.42.2-4 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-4 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-4 install ok installed libc6:amd64 libc6 2.43-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.3-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.3-1 install ok installed libmd0:amd64 libmd0 1.2.0-2 install ok installed libmount1:amd64 libmount1 2.42.2-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1+b2 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1 install ok installed libselinux1:amd64 libselinux1 3.11-2 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.2-4 install ok installed libssl3t64:amd64 libssl3t64 3.6.3-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-1 install ok installed libsystemd0:amd64 libsystemd0 261.2-1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 261.2-1 install ok installed libuuid1:amd64 libuuid1 2.42.2-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.2-4 install ok installed login.defs login.defs 1:4.19.3-2 install ok installed mawk mawk 1.3.4.20260302-1 install ok installed mount mount 2.42.2-4 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.3-1 install ok installed passwd passwd 1:4.19.3-2 install ok installed perl-base perl-base 5.42.3-1 install ok installed sed sed 4.9-3 install ok installed sqv sqv 1.4.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-1 install ok installed tar tar 1.35+dfsg-5 install ok installed tzdata tzdata 2026c-1 install ok installed util-linux util-linux 2.42.2-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-3 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m6.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m6.2s INFO: Running scripts is_testable 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/is_testable_uninstallable'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/is_testable_uninstallable'] 0m6.2s INFO: Running scripts pre_test 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_test_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_test_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_test_root_password'] 0m6.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_test_root_password'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'show', '--no-all-versions', 'atropos'] 0m6.5s DUMP: Package: atropos Source: atropos (1.1.32+dfsg-2) Version: 1.1.32+dfsg-2+b3 Installed-Size: 1279 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), python3 (<< 3.15), python3 (>= 3.13~), python3:any, python3-pysam Recommends: python3-jinja2 Description-en: NGS read trimming tool that is specific, sensitive, and speedy Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer, with the primary improvements being: . 1. Multi-threading support, including an extremely fast "parallel write" mode. 2. Implementation of a new insert alignment-based trimming algorithm for paired-end reads that is substantially more sensitive and specific than the original Cutadapt adapter alignment-based algorithm. This algorithm can also correct mismatches between the overlapping portions of the reads. 3. Options for trimming specific types of data (miRNA, bisulfite-seq). 4. A new command ('detect') that will detect adapter sequences and other potential contaminants. 5. A new command ('error') that will estimate the sequencing error rate, which helps to select the appropriate adapter- and quality- trimming parameter values. 6. A new command ('qc') that generates read statistics similar to FastQC. The trim command can also compute read statistics both before and after trimming (using the '--stats' option). 7. Improved summary reports, including support for serialization formats (JSON, YAML, pickle), support for user-defined templates (via the optional Jinja2 dependency), and integration with MultiQC. 8. The ability to merge overlapping reads (this is experimental and the functionality is limited). 9. The ability to write the summary report and log messages to separate files. 10. The ability to read SAM/BAM files and read/write interleaved FASTQ files. 11. Direct trimming of reads from an SRA accession. 12. A progress bar, and other minor usability enhancements. Description-md5: 6d8a51e28a71effebfff42f9cbd1e5bc Homepage: https://github.com/jdidion/atropos Section: science Priority: optional Filename: pool/main/a/atropos/atropos_1.1.32+dfsg-2+b3_amd64.deb Size: 265400 MD5sum: d23597f5ddefa7b15c46675d948b8840 SHA256: 6ae34676dcc1712eb4844fb9d8ccf0af1b58f53b2ebe89756f92a96a9261496e 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'show', '--no-all-versions', 'atropos'] 0m6.5s INFO: apt-cache knows about the following packages: atropos 0m6.5s INFO: Running scripts pre_install 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m6.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m6.6s DUMP: atropos: Installed: (none) Candidate: 1.1.32+dfsg-2+b3 Version table: 1.1.32+dfsg-2+b3 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos'] 0m12.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libdeflate0 libexpat1 libffi8 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-minimal python3-pysam python3.14 python3.14-minimal readline-common Suggested packages: gnutls-bin krb5-doc krb5-user python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binutils binfmt-support readline-doc Recommended packages: python3-jinja2 ca-certificates krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules The following NEW packages will be installed: atropos libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libdeflate0 libexpat1 libffi8 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-minimal python3-pysam python3.14 python3.14-minimal readline-common 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After this operation, 90.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.8.3-1 [127 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libpython3.14-minimal amd64 3.14.7-1 [899 kB] Get:3 http://deb.debian.org/debian forky/main amd64 python3.14-minimal amd64 3.14.7-1 [2714 kB] Get:4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.14.7-3 [25.3 kB] Get:5 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get:6 http://deb.debian.org/debian forky/main amd64 netbase all 6.6 [10.3 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.8.0-2 [32.5 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libncursesw6 amd64 6.6+20260608-2 [137 kB] Get:9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-4 [74.8 kB] Get:10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Get:11 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.53.4-2 [974 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libpython3.14-stdlib amd64 3.14.7-1 [2356 kB] Get:13 http://deb.debian.org/debian forky/main amd64 python3.14 amd64 3.14.7-1 [861 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.14.7-3 [8252 B] Get:15 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.14.7-3 [26.0 kB] Get:16 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.17.0-1 [68.1 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.2.0-4+b1 [312 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-5 [109 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.26.5-1 [482 kB] Get:22 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.21.0-2+b1 [49.3 kB] Get:23 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.13-1 [1546 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.4-1+b1 [19.5 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:27 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:28 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:29 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-11 [55.2 kB] Get:32 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.14+dfsg-2 [200 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:34 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.24.0-1 [23.9 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.23.3-1 [61.7 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-6 [253 kB] Get:37 http://deb.debian.org/debian forky/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:38 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:39 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:40 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:41 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:42 http://deb.debian.org/debian forky/main amd64 python3-pysam amd64 0.23.3+ds-2+b1 [4456 kB] Get:43 http://deb.debian.org/debian forky/main amd64 atropos amd64 1.1.32+dfsg-2+b3 [265 kB] Fetched 18.7 MB in 0s (38.4 MB/s) Selecting previously unselected package libexpat1: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 ... 4980 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.3-1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.7-1_amd64.deb ... Unpacking libpython3.14-minimal:amd64 (3.14.7-1) ... Selecting previously unselected package python3.14-minimal. Preparing to unpack .../python3.14-minimal_3.14.7-1_amd64.deb ... Unpacking python3.14-minimal (3.14.7-1) ... Setting up libpython3.14-minimal:amd64 (3.14.7-1) ... Setting up libexpat1:amd64 (2.8.3-1) ... Setting up python3.14-minimal (3.14.7-1) ... Selecting previously unselected package python3-minimal. (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 ... 5336 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.14.7-3_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.53.4-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.53.4-2) ... Selecting previously unselected package libpython3.14-stdlib:amd64. Preparing to unpack .../08-libpython3.14-stdlib_3.14.7-1_amd64.deb ... Unpacking libpython3.14-stdlib:amd64 (3.14.7-1) ... 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Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-11) ... Setting up libunistring5:amd64 (1.4.2-1) ... Setting up libncursesw6:amd64 (6.6+20260608-2) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-11) ... Setting up libnghttp3-9:amd64 (1.17.0-1) ... Setting up libffi8:amd64 (3.8.0-2) ... Setting up libtasn1-6:amd64 (4.21.0-2+b1) ... Setting up netbase (6.6) ... Setting up libngtcp2-16:amd64 (1.24.0-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-6) ... Setting up readline-common (8.3-4) ... Setting up libldap2:amd64 (2.6.14+dfsg-2) ... Setting up libidn2-0:amd64 (2.3.8-5) ... Setting up libp11-kit0:amd64 (0.26.5-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libreadline8t64:amd64 (8.3-4) ... Setting up libgnutls30t64:amd64 (3.8.13-1) ... Setting up libpython3.14-stdlib:amd64 (3.14.7-1) ... Setting up libpsl5t64:amd64 (0.23.3-1) ... Setting up python3.14 (3.14.7-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Setting up libpython3-stdlib:amd64 (3.14.7-3) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up python3 (3.14.7-3) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up python3-pysam (0.23.3+ds-2+b1) ... Setting up atropos (1.1.32+dfsg-2+b3) ... Processing triggers for libc-bin (2.43-4) ... 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos'] 0m12.7s INFO: Running scripts post_install 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m12.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m13.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m13.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpepgie0sc to sid 0m13.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m13.1s INFO: Running scripts pre_distupgrade 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'update'] 0m16.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [193 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.7 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7721 kB] Fetched 18.7 MB in 2s (9052 kB/s) Reading package lists... 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'update'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-yf', 'dist-upgrade'] 0m19.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: atropos bsdutils gcc-16-base libblkid1 libcap-ng0 libcurl3t64-gnutls libcurl4-gnutls libexpat1 libgcc-s1 libmount1 libpcre2-8-0 libsmartcols1 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 login mount openssl-provider-legacy util-linux 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7922 kB of archives. After this operation, 130 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.42.3-1 [34.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.42.3-1 [185 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.42.3-1 [230 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.42.3-1 [152 kB] Get:5 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.42.3-1 [1246 kB] Get:6 http://deb.debian.org/debian sid/main amd64 mount amd64 2.42.3-1 [169 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 262~rc1-2 [511 kB] Get:8 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.42.3-1 [121 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.8.4-1 [130 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-16-base amd64 16.2.0-2 [38.4 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 16.2.0-2 [823 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 16.2.0-2 [74.1 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.9.5-2 [18.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.48-2 [312 kB] Get:15 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.6.4-1 [326 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.6.4-1 [2614 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 262~rc1-2 [148 kB] Get:18 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.42.3-1 [92.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 atropos amd64 1.1.32+dfsg-2+b4 [221 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libcurl4-gnutls amd64 8.22.0-1 [457 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.22.0-1 [17.8 kB] Fetched 7922 kB in 0s (81.5 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6584 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.6.4-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.6.4-1) over (3.6.3-1) ... Setting up libssl3t64:amd64 (3.6.4-1) ... (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 ... 6584 files and directories currently installed.) Preparing to unpack .../libudev1_262~rc1-2_amd64.deb ... Unpacking libudev1:amd64 (262~rc1-2) over (261.2-1) ... Setting up libudev1:amd64 (262~rc1-2) ... (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 ... 6584 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.42.3-1_amd64.deb ... Unpacking bsdutils (1:2.42.3-1) over (1:2.42.2-4) ... Preparing to unpack .../atropos_1.1.32+dfsg-2+b4_amd64.deb ... Unpacking atropos (1.1.32+dfsg-2+b4) over (1.1.32+dfsg-2+b3) ... Preparing to unpack .../libcurl4-gnutls_8.22.0-1_amd64.deb ... Unpacking libcurl4-gnutls:amd64 (8.22.0-1) over (8.21.0-2) ... Preparing to unpack .../libcurl3t64-gnutls_8.22.0-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.22.0-1) over (8.21.0-2) ... Setting up libexpat1:amd64 (2.8.4-1) ... Setting up libcurl4-gnutls:amd64 (8.22.0-1) ... Setting up bsdutils (1:2.42.3-1) ... Setting up atropos (1.1.32+dfsg-2+b4) ... Setting up libcurl3t64-gnutls:amd64 (8.22.0-1) ... Setting up mount (2.42.3-1) ... Setting up login (1:4.16.0-2+really2.42.3-1) ... Processing triggers for libselinux1:amd64 (3.11-2) ... Processing triggers for libc-bin (2.43-4) ... 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-yf', 'dist-upgrade'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.8s DUMP: d1083c5fb295af10c92e66d7bb7d8617 - 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'show', '--no-all-versions', 'atropos'] 0m20.1s DUMP: Package: atropos Source: atropos (1.1.32+dfsg-2) Version: 1.1.32+dfsg-2+b4 Installed-Size: 923 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), python3 (<< 3.15), python3 (>= 3.14~), python3:any, python3-pysam Recommends: python3-jinja2 Description-en: NGS read trimming tool that is specific, sensitive, and speedy Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer, with the primary improvements being: . 1. Multi-threading support, including an extremely fast "parallel write" mode. 2. Implementation of a new insert alignment-based trimming algorithm for paired-end reads that is substantially more sensitive and specific than the original Cutadapt adapter alignment-based algorithm. This algorithm can also correct mismatches between the overlapping portions of the reads. 3. Options for trimming specific types of data (miRNA, bisulfite-seq). 4. A new command ('detect') that will detect adapter sequences and other potential contaminants. 5. A new command ('error') that will estimate the sequencing error rate, which helps to select the appropriate adapter- and quality- trimming parameter values. 6. A new command ('qc') that generates read statistics similar to FastQC. The trim command can also compute read statistics both before and after trimming (using the '--stats' option). 7. Improved summary reports, including support for serialization formats (JSON, YAML, pickle), support for user-defined templates (via the optional Jinja2 dependency), and integration with MultiQC. 8. The ability to merge overlapping reads (this is experimental and the functionality is limited). 9. The ability to write the summary report and log messages to separate files. 10. The ability to read SAM/BAM files and read/write interleaved FASTQ files. 11. Direct trimming of reads from an SRA accession. 12. A progress bar, and other minor usability enhancements. Description-md5: 6d8a51e28a71effebfff42f9cbd1e5bc Homepage: https://github.com/jdidion/atropos Section: science Priority: optional Filename: pool/main/a/atropos/atropos_1.1.32+dfsg-2+b4_amd64.deb Size: 221116 MD5sum: 8590d4c6098a42ed4e8db9de09aa52b2 SHA256: f3edd3fe5422eb11573133ddfad1a9772048665011438123f8970e2d25bcbc13 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'show', '--no-all-versions', 'atropos'] 0m20.1s INFO: apt-cache knows about the following packages: atropos 0m20.1s INFO: Running scripts pre_install 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m20.2s 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: 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m20.2s DUMP: atropos: Installed: 1.1.32+dfsg-2+b4 Candidate: 1.1.32+dfsg-2+b4 Version table: *** 1.1.32+dfsg-2+b4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... atropos is already the newest version (1.1.32+dfsg-2+b4). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos'] 0m21.0s INFO: Running scripts post_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m21.0s INFO: Running scripts post_distupgrade 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m21.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m21.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m21.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m21.8s INFO: Running scripts pre_install 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_database-server'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_exceptions'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_extras'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m21.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m21.9s DUMP: atropos: Installed: 1.1.32+dfsg-2+b4 Candidate: 1.1.32+dfsg-2+b4 Version table: *** 1.1.32+dfsg-2+b4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-cache', 'policy', 'atropos'] 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos=1.1.32+dfsg-2+b4'] 0m22.5s DUMP: Reading package lists... Building dependency tree... Reading state information... atropos is already the newest version (1.1.32+dfsg-2+b4). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', '-y', 'install', 'atropos=1.1.32+dfsg-2+b4'] 0m22.5s INFO: Running scripts post_install 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_install_exceptions'] 0m22.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m22.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m23.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', '-ac', '--ignore-obsolete'] 0m23.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', '-ac', '--ignore-obsolete'] 0m23.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.9s DUMP: 0.17.5+b5 0m23.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.9s INFO: Running adequate version 0.17.5+b5 now. 0m23.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'atropos'] 0m24.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'atropos'] 0m24.0s INFO: Running scripts pre_remove 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/pre_remove_exceptions'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.7s DUMP: install ok installed apt apt 3.3.3 install ok installed atropos atropos 1.1.32+dfsg-2+b4 install ok installed base-files base-files 14.2 install ok installed base-passwd base-passwd 3.6.8 install ok installed bash bash 5.3-3+b1 install ok installed bsdutils bsdutils 1:2.42.3-1 install ok installed coreutils coreutils 9.10-1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.92 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.24 install ok installed diffutils diffutils 1:3.12-1 install ok installed dpkg dpkg 1.23.7 install ok installed findutils findutils 4.11.0-2 install ok installed gcc-16-base:amd64 gcc-16-base 16.2.0-2 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.14-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69+nmu1 install ok installed libacl1:amd64 libacl1 2.4.0-1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.3.3 install ok installed libattr1:amd64 libattr1 1:2.6.0-1 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1+b1 install ok installed libblkid1:amd64 libblkid1 2.42.3-1 install ok installed libbrotli1:amd64 libbrotli1 1.2.0-4+b1 install ok installed libbsd0:amd64 libbsd0 0.12.2-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6+b2 install ok installed libc-bin libc-bin 2.43-4 install ok installed libc-gconv-modules-extra:amd64 libc-gconv-modules-extra 2.43-4 install ok installed libc6:amd64 libc6 2.43-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.9.5-2 install ok installed libcom-err2:amd64 libcom-err2 1.47.4-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.5.2+20251210-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.22.0-1 install ok installed libcurl4-gnutls:amd64 libcurl4-gnutls 8.22.0-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-11+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.283 install ok installed libdeflate0:amd64 libdeflate0 1.25-1 install ok installed libexpat1:amd64 libexpat1 2.8.4-1 install ok installed libffi8:amd64 libffi8 3.8.0-2 install ok installed libgcc-s1:amd64 libgcc-s1 16.2.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.13-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.22.1-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.22.1+ds2-1+b2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.6-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.22.1-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-6+b2 install ok installed libkrb5-3:amd64 libkrb5-3 1.22.1-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.22.1-3 install ok installed libldap2:amd64 libldap2 2.6.14+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-10 install ok installed liblzma5:amd64 liblzma5 5.8.3-1 install ok installed libmd0:amd64 libmd0 1.2.0-2 install ok installed libmount1:amd64 libmount1 2.42.3-1 install ok installed libncursesw6:amd64 libncursesw6 6.6+20260608-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.70.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.17.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.24.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.24.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.26.5-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-8 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-8 install ok installed libpam-runtime libpam-runtime 1.7.0-8 install ok installed libpam0g:amd64 libpam0g 1.7.0-8 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.48-2 install ok installed libpsl5t64:amd64 libpsl5t64 0.23.3-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.14.7-3 install ok installed libpython3.14-minimal:amd64 libpython3.14-minimal 3.14.7-1 install ok installed libpython3.14-stdlib:amd64 libpython3.14-stdlib 3.14.7-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.3-4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-11 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-11 install ok installed libseccomp2:amd64 libseccomp2 2.6.1-1 install ok installed libselinux1:amd64 libselinux1 3.11-2 install ok installed libsemanage-common libsemanage-common 3.11-1 install ok installed libsemanage2:amd64 libsemanage2 3.11-1 install ok installed libsepol2:amd64 libsepol2 3.11-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.42.3-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.53.4-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-6 install ok installed libssl3t64:amd64 libssl3t64 3.6.4-1 install ok installed libstdc++6:amd64 libstdc++6 16.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 262~rc1-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.21.0-2+b1 install ok installed libtinfo6:amd64 libtinfo6 6.6+20260608-2 install ok installed libudev1:amd64 libudev1 262~rc1-2 install ok installed libunistring5:amd64 libunistring5 1.4.2-1 install ok installed libuuid1:amd64 libuuid1 2.42.3-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-4 install ok installed login login 1:4.16.0-2+really2.42.3-1 install ok installed login.defs login.defs 1:4.19.3-2 install ok installed mawk mawk 1.3.4.20260302-1 install ok installed media-types media-types 14.0.0 install ok installed mount mount 2.42.3-1 install ok installed ncurses-base ncurses-base 6.6+20260608-2 install ok installed ncurses-bin ncurses-bin 6.6+20260608-2 install ok installed netbase netbase 6.6 install ok installed openssl-provider-legacy openssl-provider-legacy 3.6.4-1 install ok installed passwd passwd 1:4.19.3-2 install ok installed perl-base perl-base 5.42.3-1 install ok installed python3 python3 3.14.7-3 install ok installed python3-minimal python3-minimal 3.14.7-3 install ok installed python3-pysam python3-pysam 0.23.3+ds-2+b1 install ok installed python3.14 python3.14 3.14.7-1 install ok installed python3.14-minimal python3.14-minimal 3.14.7-1 install ok installed readline-common readline-common 8.3-4 install ok installed sed sed 4.9-3 install ok installed sqv sqv 1.4.0-1 install ok installed sysvinit-utils sysvinit-utils 3.18-1 install ok installed tar tar 1.35+dfsg-5 install ok installed tzdata tzdata 2026c-1 install ok installed util-linux util-linux 2.42.3-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.2-3 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'remove', '--allow-remove-essential', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-pysam', 'python3.14', 'python3.14-minimal', 'readline-common', 'atropos'] 0m26.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages will be REMOVED: atropos libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libdeflate0 libexpat1 libffi8 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib libreadline8t64 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-minimal python3-pysam python3.14 python3.14-minimal readline-common 0 upgraded, 0 newly installed, 43 to remove and 0 not upgraded. After this operation, 90.6 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 ... 6581 files and directories currently installed.) Removing atropos (1.1.32+dfsg-2+b4) ... Removing python3-pysam (0.23.3+ds-2+b1) ... Removing libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Removing libcurl3t64-gnutls:amd64 (8.22.0-1) ... Removing libcurl4-gnutls:amd64 (8.22.0-1) ... Removing libbrotli1:amd64 (1.2.0-4+b1) ... Removing libgssapi-krb5-2:amd64 (1.22.1-3) ... Removing libkrb5-3:amd64 (1.22.1-3) ... Removing libcom-err2:amd64 (1.47.4-1+b1) ... Removing libdeflate0:amd64 (1.25-1) ... Removing python3 (3.14.7-3) ... Removing python3.14 (3.14.7-1) ... Removing python3-minimal (3.14.7-3) ... Removing python3.14-minimal (3.14.7-1) ... Removing libexpat1:amd64 (2.8.4-1) ... Removing libpython3-stdlib:amd64 (3.14.7-3) ... Removing libpython3.14-stdlib:amd64 (3.14.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Removing libgnutls30t64:amd64 (3.8.13-1) ... Removing libp11-kit0:amd64 (0.26.5-1) ... Removing libffi8:amd64 (3.8.0-2) ... Removing libhtscodecs2:amd64 (1.6.6-1) ... Removing libpsl5t64:amd64 (0.23.3-1) ... Removing libidn2-0:amd64 (2.3.8-5) ... Removing libk5crypto3:amd64 (1.22.1-3) ... Removing libkeyutils1:amd64 (1.6.3-6+b2) ... Removing libkrb5support0:amd64 (1.22.1-3) ... Removing libldap2:amd64 (2.6.14+dfsg-2) ... Removing libncursesw6:amd64 (6.6+20260608-2) ... Removing libnghttp2-14:amd64 (1.70.0-1) ... Removing libnghttp3-9:amd64 (1.17.0-1) ... Removing libngtcp2-16:amd64 (1.24.0-1) ... Removing libpython3.14-minimal:amd64 (3.14.7-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.3-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsasl2-2:amd64 (2.1.28+dfsg1-11) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-11) ... Removing libsqlite3-0:amd64 (3.53.4-2) ... Removing libssh2-1t64:amd64 (1.11.1-6) ... Removing libtasn1-6:amd64 (4.21.0-2+b1) ... Removing libunistring5:amd64 (1.4.2-1) ... Removing media-types (14.0.0) ... Removing netbase (6.6) ... Removing readline-common (8.3-4) ... Processing triggers for libc-bin (2.43-4) ... 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'remove', '--allow-remove-essential', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-pysam', 'python3.14', 'python3.14-minimal', 'readline-common', 'atropos'] 0m26.4s INFO: Running scripts post_remove 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_remove_exceptions'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_remove_exceptions'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-pysam', 'python3.14', 'python3.14-minimal', 'readline-common'] 0m26.4s DUMP: dpkg: warning: ignoring request to remove libbrotli1 which is not installed dpkg: warning: ignoring request to remove libcom-err2 which is not installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which is not installed dpkg: warning: ignoring request to remove libcurl4-gnutls which is not installed dpkg: warning: ignoring request to remove libdeflate0 which is not installed dpkg: warning: ignoring request to remove libexpat1 which is not installed dpkg: warning: ignoring request to remove libffi8 which is not installed dpkg: warning: ignoring request to remove libgnutls30t64 which is not installed (Reading database ... 4986 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.22.1-3) ... dpkg: warning: ignoring request to remove libhts3t64 which is not installed dpkg: warning: ignoring request to remove libhtscodecs2 which is not installed dpkg: warning: ignoring request to remove libidn2-0 which is not installed dpkg: warning: ignoring request to remove libk5crypto3 which is not installed dpkg: warning: ignoring request to remove libkeyutils1 which is not installed dpkg: warning: ignoring request to remove libkrb5-3 which is not installed dpkg: warning: ignoring request to remove libkrb5support0 which is not installed dpkg: warning: ignoring request to remove libldap2 which is not installed dpkg: warning: ignoring request to remove libncursesw6 which is not installed dpkg: warning: ignoring request to remove libnghttp2-14 which is not installed dpkg: warning: ignoring request to remove libnghttp3-9 which is not installed dpkg: warning: ignoring request to remove libngtcp2-16 which is not installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which is not installed dpkg: warning: ignoring request to remove libp11-kit0 which is not installed dpkg: warning: ignoring request to remove libpsl5t64 which is not installed dpkg: warning: ignoring request to remove libpython3-stdlib which is not installed Purging configuration files for libpython3.14-minimal:amd64 (3.14.7-1) ... dpkg: warning: ignoring request to remove libpython3.14-stdlib which is not installed Purging configuration files for libreadline8t64:amd64 (8.3-4) ... dpkg: warning: ignoring request to remove libsasl2-2 which is not installed dpkg: warning: ignoring request to remove libsasl2-modules-db which is not installed dpkg: warning: ignoring request to remove libsqlite3-0 which is not installed dpkg: warning: ignoring request to remove libssh2-1t64 which is not installed dpkg: warning: ignoring request to remove libtasn1-6 which is not installed dpkg: warning: ignoring request to remove libunistring5 which is not installed Purging configuration files for media-types (14.0.0) ... Purging configuration files for netbase (6.6) ... Purging configuration files for python3 (3.14.7-3) ... dpkg: warning: ignoring request to remove python3-minimal which is not installed dpkg: warning: ignoring request to remove python3-pysam which is not installed dpkg: warning: ignoring request to remove python3.14 which is not installed Purging configuration files for python3.14-minimal (3.14.7-1) ... Purging configuration files for readline-common (8.3-4) ... 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.14-minimal:amd64', 'libpython3.14-stdlib:amd64', 'libreadline8t64:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-pysam', 'python3.14', 'python3.14-minimal', 'readline-common'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', 'atropos'] 0m26.4s DUMP: dpkg: warning: ignoring request to remove atropos which is not installed 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', 'atropos'] 0m26.4s INFO: Running scripts post_purge 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_purge_exceptions'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_purge_exceptions'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', '--pending'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--purge', '--pending'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--remove', '--pending'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg', '--remove', '--pending'] 0m26.5s INFO: Running scripts post_test 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_test_exceptions'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'tmp/scripts/post_test_exceptions'] 0m26.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m26.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-divert', '--list'] 0m26.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'dpkg-divert', '--list'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'clean'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpepgie0sc', 'apt-get', 'clean'] 0m26.8s DEBUG: Recording chroot state 0m27.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/shm'] 0m27.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/shm'] 0m27.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/console'] 0m27.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/console'] 0m27.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/ptmx'] 0m27.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/ptmx'] 0m27.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts'] 0m27.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/dev/pts'] 0m27.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/proc'] 0m28.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpepgie0sc/proc'] 0m28.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m28.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpepgie0sc'] 0m28.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpepgie0sc 0m28.1s INFO: PASS: Upgrading between Debian distributions. 0m28.1s INFO: PASS: All tests. 0m28.1s INFO: piuparts run ends. ret=0 End: 2026-09-04 10:20:56 GMT