Start: 2024-04-09 04:25:59 GMT Package: iva Version: 1.0.11+ds-5 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-5_amd64.deb Size: 8581624 MD5sum: 81641314ba9e9e3b5e100a7443802397 SHA256: 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef 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-log-alternatives --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/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt iva=1.0.11+ds-5 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 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --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/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt iva=1.0.11+ds-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpgbpzpng1 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpgbpzpng1 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpgbpzpng1/tmp/scripts/ 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpgbpzpng1/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'update'] 0m5.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9913 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7197 kB] Fetched 17.3 MB in 4s (4114 kB/s) Reading package lists... 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'update'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', '-yf', 'dist-upgrade'] 0m9.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: libdb5.3t64 The following packages will be upgraded: bsdutils libblkid1 libgnutls30t64 libmount1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libselinux1 libsmartcols1 libuuid1 mount perl-base util-linux 14 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 6357 kB of archives. After this operation, 1604 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40-5 [100 kB] Get:2 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2+b2 [1644 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40-5 [32.0 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40-5 [163 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40-5 [194 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40-5 [135 kB] Get:7 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40-5 [1205 kB] Get:8 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40-5 [147 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b2 [74.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.5-2 [1437 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6357 kB in 0s (73.0 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 ... 5216 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40-5_amd64.deb ... Unpacking bsdutils (1:2.40-5) over (1:2.39.3-11) ... Setting up bsdutils (1:2.40-5) ... (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 ... 5216 files and directories currently installed.) Preparing to unpack .../perl-base_5.38.2-3.2+b2_amd64.deb ... Unpacking perl-base (5.38.2-3.2+b2) over (5.38.2-3.2) ... Setting up perl-base (5.38.2-3.2+b2) ... (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 ... 5217 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40-5_amd64.deb ... Unpacking libuuid1:amd64 (2.40-5) over (2.39.3-11) ... Setting up libuuid1:amd64 (2.40-5) ... (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 ... 5217 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40-5_amd64.deb ... Unpacking libblkid1:amd64 (2.40-5) over (2.39.3-11) ... Setting up libblkid1:amd64 (2.40-5) ... (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 ... 5217 files and directories currently installed.) Preparing to unpack .../libmount1_2.40-5_amd64.deb ... Unpacking libmount1:amd64 (2.40-5) over (2.39.3-11) ... Setting up libmount1:amd64 (2.40-5) ... (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 ... 5217 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40-5_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40-5) over (2.39.3-11) ... Setting up libsmartcols1:amd64 (2.40-5) ... (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 ... 5217 files and directories currently installed.) Preparing to unpack .../util-linux_2.40-5_amd64.deb ... Unpacking util-linux (2.40-5) over (2.39.3-11) ... Setting up util-linux (2.40-5) ... (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 ... 5191 files and directories currently installed.) Preparing to unpack .../mount_2.40-5_amd64.deb ... Unpacking mount (2.40-5) over (2.39.3-11) ... Preparing to unpack .../libselinux1_3.5-2+b2_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2+b2) over (3.5-2+b1) ... Setting up libselinux1:amd64 (3.5-2+b2) ... Selecting previously unselected package libdb5.3t64: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 ... 5191 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... (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 ... 5197 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-7_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-7) over (1.5.3-6) ... Setting up libpam0g:amd64 (1.5.3-7) ... (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 ... 5197 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.5.3-6) ... Setting up libpam-modules-bin (1.5.3-7) ... (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 ... 5197 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.5.3-6) ... Setting up libpam-modules:amd64 (1.5.3-7) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-7_all.deb ... Unpacking libpam-runtime (1.5.3-7) over (1.5.3-6) ... Setting up libpam-runtime (1.5.3-7) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.5-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.5-2) over (3.8.5-1) ... Setting up libgnutls30t64:amd64 (3.8.5-2) ... Setting up mount (2.40-5) ... Processing triggers for libc-bin (2.37-15.1) ... 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', '-yf', 'dist-upgrade'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.9s DUMP: cc0cc9baadddf8028fba114b539e5410 - 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.9s INFO: Running scripts post_setup 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_dummy_users'] 0m10.7s 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 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_dummy_users'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_forbid_home'] 0m10.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_forbid_home'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.8s 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' 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_minimize'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_minimize'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_zz_backports'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_setup_zz_backports'] 0m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'clean'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'clean'] 0m10.8s DEBUG: Recording chroot state 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.5s DUMP: install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-5 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-divert', '--list'] 0m11.5s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-divert', '--list'] 0m11.5s INFO: Running scripts is_testable 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/is_testable_uninstallable'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/is_testable_uninstallable'] 0m11.5s INFO: apt-cache does not know about any of the requested packages 0m11.5s INFO: Running scripts pre_test 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_test_exceptions'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_test_exceptions'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_test_root_password'] 0m11.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_test_root_password'] 0m11.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m12.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m12.7s DEBUG: No broken symlinks as far as we can find. 0m12.7s INFO: Running scripts pre_install 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_database-server'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_database-server'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_exceptions'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_exceptions'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_extras'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_extras'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_log_alternatives'] 0m12.7s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_install_log_alternatives'] 0m12.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m13.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m13.8s DEBUG: No broken symlinks as far as we can find. 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-cache', 'policy'] 0m15.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-cache', 'policy'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-cache', 'policy', 'iva'] 0m15.0s DUMP: iva: Installed: (none) Candidate: 1.0.11+ds-5 Version table: 1.0.11+ds-5 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-cache', 'policy', 'iva'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-5'] 0m38.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq gawk java-common kmc libbambamc0 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 media-types mummer netbase openjdk-17-jre-headless openssl perl perl-modules-5.38 python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3.11 python3.11-minimal readline-common samtools smalt Suggested packages: default-jre gawk-doc gdbm-l10n krb5-doc krb5-user liblcms2-utils pcscd sensible-utils libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv gcc gfortran python3-dev python3-pytest python3-setuptools python3.11-venv python3.11-doc binutils binfmt-support readline-doc cwltool Recommended packages: r-base-core bioperl trimmomatic krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml The following NEW packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq gawk iva java-common kmc libbambamc0 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 media-types mummer netbase openjdk-17-jre-headless openssl perl perl-modules-5.38 python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3.11 python3.11-minimal readline-common samtools smalt 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 91.7 MB of archives. After this operation, 409 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2+b2 [4279 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2+b2 [236 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:7 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3+b3 [817 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3+b3 [1879 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:15 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:16 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3+b3 [1792 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3+b3 [597 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:22 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:23 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:24 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:25 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:26 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:27 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get:32 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.11~7ea-1+b1 [43.8 MB] Get:33 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:34 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:39 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.61.0-1 [75.3 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:46 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.7.1-2 [432 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:53 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get:54 http://deb.debian.org/debian sid/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-networkx all 2.8.8-2 [1425 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get:58 http://deb.debian.org/debian sid/main amd64 kmc amd64 3.2.4+dfsg-1 [1015 kB] Get:59 http://deb.debian.org/debian sid/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:61 http://deb.debian.org/debian sid/main amd64 smalt amd64 0.7.6-13 [115 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get:64 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:65 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-6 [5472 kB] Get:66 http://deb.debian.org/debian sid/main amd64 iva amd64 1.0.11+ds-5 [8582 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 91.7 MB in 1s (117 MB/s) Selecting previously unselected package perl-modules-5.38. (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 ... 5205 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libgdbm-compat4t64:amd64. 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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 (8.2-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../8-libsigsegv2_2.14-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1) ... Setting up libmpfr6:amd64 (4.2.1-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libsigsegv2:amd64 (2.14-1) ... Selecting previously unselected package gawk. (Reading database ... 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Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up openssl (3.2.1-3) ... Setting up kmc (3.2.4+dfsg-1) ... Setting up smalt (0.7.6-13) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libpython3.11-stdlib:amd64 (3.11.8-3+b3) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.38.2-3.2+b2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up mummer (3.23+dfsg-8) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.8-3+b3) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-2) ... Setting up python3 (3.11.8-1) ... Setting up python3-packaging (24.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-networkx (2.8.8-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up fastaq (3.17.0-6) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up default-jre-headless (2:1.17-75) ... Setting up iva (1.0.11+ds-5) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-5'] 0m38.2s INFO: Running scripts post_install 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_install_exceptions'] 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_install_exceptions'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_install_log_alternatives'] 0m38.3s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=gawk: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --quiet --install /usr/bin/awk awk /usr/bin/gawk 10 --slave /usr/share/man/man1/awk.1.gz awk.1.gz /usr/share/man/man1/gawk.1.gz --slave /usr/bin/nawk nawk /usr/bin/gawk --slave /usr/share/man/man1/nawk.1.gz nawk.1.gz /usr/share/man/man1/gawk.1.gz LOG-ALTERNATIVES: dpkg=libblas3: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=perl: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-17-openjdk-amd64/bin/java 1711 --slave /usr/share/man/man1/java.1.gz java.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/java.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/bin/jpackage jpackage /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage 1711 --slave /usr/share/man/man1/jpackage.1.gz jpackage.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/jpackage.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/bin/keytool keytool /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool 1711 --slave /usr/share/man/man1/keytool.1.gz keytool.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/keytool.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/bin/rmiregistry rmiregistry /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry 1711 --slave /usr/share/man/man1/rmiregistry.1.gz rmiregistry.1.gz /usr/lib/jvm/java-17-openjdk-amd64/man/man1/rmiregistry.1.gz LOG-ALTERNATIVES: dpkg=openjdk-17-jre-headless: piuparts=iva=1.0.11+ds-5: /usr/bin/update-alternatives --install /usr/bin/jexec jexec /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec 1711 --slave /usr/share/binfmts/jar jexec-binfmt /usr/lib/jvm/java-17-openjdk-amd64/lib/jar.binfmt 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_install_log_alternatives'] 0m38.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m39.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m40.9s DEBUG: No broken symlinks as far as we can find. 0m40.9s INFO: /bin converted to /usr/bin by /usr merge 0m40.9s INFO: /lib converted to /usr/lib by /usr merge 0m40.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m40.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m40.9s INFO: /sbin converted to /usr/sbin by /usr merge 0m41.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', '-ac', '--ignore-obsolete'] 0m43.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', '-ac', '--ignore-obsolete'] 0m43.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.7s DUMP: 0.15.6 0m43.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.7s INFO: Running adequate version 0.15.6 now. 0m43.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'iva'] 0m43.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'iva'] 0m43.7s INFO: Running scripts pre_remove 0m43.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m43.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m43.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_exceptions'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/pre_remove_exceptions'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.5s DUMP: install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed fastaq fastaq 3.17.0-6 install ok installed findutils findutils 4.9.0-5 install ok installed gawk gawk 1:5.2.1-2+b1 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed iva iva 1.0.11+ds-5 install ok installed java-common java-common 0.75 install ok installed kmc kmc 3.2.4+dfsg-1 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-6+b1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.7.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1+b1 install ok installed libgfortran5:amd64 libgfortran5 14-20240330-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.61.0-1 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.99-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.3-1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2+b2 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3+b3 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3+b3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.2-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b2 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40-5 install ok installed mummer mummer 3.23+dfsg-8 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.11~7ea-1+b1 install ok installed openssl openssl 3.2.1-3 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2+b2 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed python3 python3 3.11.8-1 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-networkx python3-networkx 2.8.8-2 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-6 install ok installed python3-packaging python3-packaging 24.0-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b2 install ok installed python3.11 python3.11 3.11.8-3+b3 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3+b3 install ok installed readline-common readline-common 8.2-4 install ok installed samtools samtools 1.19.2-1+b1 install ok installed sed sed 4.9-2 install ok installed smalt smalt 0.7.6-13 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'gawk', 'java-common', 'kmc', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'smalt', 'iva'] 0m48.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates ca-certificates-java default-jre-headless fastaq gawk iva java-common kmc libbambamc0 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.38t64 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 media-types mummer netbase openjdk-17-jre-headless openssl perl perl-modules-5.38 python3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3.11 python3.11-minimal readline-common samtools smalt 0 upgraded, 0 newly installed, 66 to remove and 0 not upgraded. After this operation, 409 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 ... 12022 files and directories currently installed.) Removing iva (1.0.11+ds-5) ... Removing default-jre-headless (2:1.17-75) ... Removing openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing fastaq (3.17.0-6) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2+b1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing java-common (0.75) ... Removing kmc (3.2.4+dfsg-1) ... Removing smalt (0.7.6-13) ... Removing libbambamc0:amd64 (0.0.50-6+b1) ... Removing python3-numpy (1:1.26.4+ds-6) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing samtools (1.19.2-1+b1) ... Removing python3-pysam (0.22.0+ds-1+b2) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.7.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libdeflate0:amd64 (1.20-1) ... Removing python3-networkx (2.8.8-2) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-packaging (24.0-1) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.8-3+b3) ... Removing python3-minimal (3.11.8-1) ... Removing python3.11-minimal (3.11.8-3+b3) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing perl (5.38.2-3.2+b2) ... Removing libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Removing libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Removing libgdbm6t64:amd64 (1.23-5.1+b1) ... Removing libgfortran5:amd64 (14-20240330-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libkrb5-3:amd64 (1.20.1-6+b1) ... Removing libk5crypto3:amd64 (1.20.1-6+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6+b1) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3+b3) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libnghttp2-14:amd64 (1.61.0-1) ... Removing libnss3:amd64 (2:3.99-1) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libpcsclite1:amd64 (2.0.3-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libpython3.11-minimal:amd64 (3.11.8-3+b3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libsigsegv2:amd64 (2.14-1) ... Removing libsqlite3-0:amd64 (3.45.2-1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing openssl (3.2.1-3) ... Removing perl-modules-5.38 (5.38.2-3.2) ... Removing readline-common (8.2-4) ... Processing triggers for libc-bin (2.37-15.1) ... 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'gawk', 'java-common', 'kmc', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'smalt', 'iva'] 0m48.8s INFO: Running scripts post_remove 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_remove_exceptions'] 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_remove_exceptions'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'gawk', 'java-common', 'kmc', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'smalt'] 0m49.0s DUMP: (Reading database ... 5255 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed Purging configuration files for gawk (1:5.2.1-2+b1) ... Purging configuration files for java-common (0.75) ... dpkg: warning: ignoring request to remove kmc which isn't installed dpkg: warning: ignoring request to remove libbambamc0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3+b3) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for netbase (6.4) ... Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.11~7ea-1+b1) ... Purging configuration files for openssl (3.2.1-3) ... Purging configuration files for perl (5.38.2-3.2+b2) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-3+b3) ... Purging configuration files for readline-common (8.2-4) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'gawk', 'java-common', 'kmc', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'smalt'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', 'iva'] 0m49.1s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', 'iva'] 0m49.1s INFO: Running scripts post_purge 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_purge_exceptions'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_purge_exceptions'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', '--pending'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--purge', '--pending'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--remove', '--pending'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg', '--remove', '--pending'] 0m49.1s INFO: Running scripts post_test 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_test_exceptions'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'tmp/scripts/post_test_exceptions'] 0m49.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m49.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m50.2s DEBUG: No broken symlinks as far as we can find. 0m50.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-divert', '--list'] 0m50.2s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'dpkg-divert', '--list'] 0m50.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'clean'] 0m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1', 'apt-get', 'clean'] 0m50.2s DEBUG: Recording chroot state 0m50.9s INFO: PASS: Installation and purging test. 0m51.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/shm'] 0m51.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/shm'] 0m51.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/console'] 0m51.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/console'] 0m51.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/ptmx'] 0m51.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/ptmx'] 0m51.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts'] 0m51.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/dev/pts'] 0m51.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/proc'] 0m51.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1/proc'] 0m51.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m51.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgbpzpng1'] 0m51.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpgbpzpng1 0m51.6s INFO: PASS: All tests. 0m51.6s INFO: piuparts run ends. ret=0 End: 2024-04-09 04:26:51 GMT