Start: 2024-12-10 03:29:11 GMT Package: iva Version: 1.0.11+ds-6 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-6_amd64.deb Size: 8581812 MD5sum: 3bb224aeb71839351829ccb0174f884c SHA256: dfc79c21433530b4e62523cb0e4ac77efd6c8f4ac8d4ba907fdc08875f8cfd93 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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt iva=1.0.11+ds-6 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt iva=1.0.11+ds-6 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmps483aocy 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmps483aocy 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps483aocy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps483aocy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmps483aocy/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmps483aocy/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/tmps483aocy/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/tmps483aocy/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmps483aocy/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmps483aocy/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'update'] 0m2.2s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9341 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6270 kB] Fetched 15.8 MB in 1s (14.7 MB/s) Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash bsdutils libblkid1 libdebconfclient0 libgpg-error0 libmount1 libsmartcols1 libunistring5 libuuid1 login mount util-linux 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4163 kB of archives. After this operation, 271 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-1 [1501 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-12 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-12 [36.0 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-12 [168 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-12 [199 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-12 [139 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-12 [1209 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-12 [155 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.2-12 [81.8 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.274 [10.1 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-2 [82.1 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4163 kB in 0s (46.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5142 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-1_amd64.deb ... Unpacking bash (5.2.37-1) over (5.2.32-1+b2) ... Setting up bash (5.2.37-1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5141 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-12_amd64.deb ... Unpacking bsdutils (1:2.40.2-12) over (1:2.40.2-11) ... Setting up bsdutils (1:2.40.2-12) ... (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 ... 5141 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-12_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libuuid1:amd64 (2.40.2-12) ... (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 ... 5141 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-12_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libblkid1:amd64 (2.40.2-12) ... (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 ... 5141 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-12_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libmount1:amd64 (2.40.2-12) ... (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 ... 5141 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-12_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libsmartcols1:amd64 (2.40.2-12) ... (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 ... 5141 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-12_amd64.deb ... Unpacking util-linux (2.40.2-12) over (2.40.2-11) ... Setting up util-linux (2.40.2-12) ... (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 ... 5138 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-12_amd64.deb ... Unpacking mount (2.40.2-12) over (2.40.2-11) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-12_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-12) over (1:4.16.0-2+really2.40.2-11) ... Preparing to unpack .../libdebconfclient0_0.274_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.274) over (0.273) ... Setting up libdebconfclient0:amd64 (0.274) ... (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 ... 5138 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.51-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.51-2) over (1.50-4) ... Setting up libgpg-error0:amd64 (1.51-2) ... (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 ... 5138 files and directories currently installed.) Preparing to unpack .../libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) over (1.2-1+b1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up mount (2.40.2-12) ... Setting up login (1:4.16.0-2+really2.40.2-12) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.40-4) ... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s DUMP: 695469f0cbe47b5af90dbdd55c0307ec - 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s INFO: Running scripts post_setup 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s 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 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.5s 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' 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_minimize'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_minimize'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_zz_backports'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_setup_zz_backports'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'clean'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'clean'] 0m5.6s DEBUG: Recording chroot state 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.16 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-divert', '--list'] 0m6.0s 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 /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 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 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 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-divert', '--list'] 0m6.0s INFO: Running scripts is_testable 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/is_testable_uninstallable'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/is_testable_uninstallable'] 0m6.0s INFO: apt-cache does not know about any of the requested packages 0m6.0s INFO: Running scripts pre_test 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_test_root_password'] 0m6.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_test_root_password'] 0m6.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m6.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m6.7s DEBUG: No broken symlinks as far as we can find. 0m6.7s INFO: Running scripts pre_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_database-server'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_database-server'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_exceptions'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_extras'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_extras'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_log_alternatives'] 0m6.8s 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 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_install_log_alternatives'] 0m6.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m7.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m7.5s DEBUG: No broken symlinks as far as we can find. 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-cache', 'policy'] 0m8.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-cache', 'policy'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-cache', 'policy', 'iva'] 0m8.2s DUMP: iva: Installed: (none) Candidate: 1.0.11+ds-6 Version table: 1.0.11+ds-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-cache', 'policy', 'iva'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-6'] 0m27.2s 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpcsclite1 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 media-types mummer netbase openjdk-21-jre-headless openssl perl perl-modules-5.40 python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3-typeguard python3-typing-extensions python3.12 python3.12-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 python-numpy-doc python3-dev python3-pytest python3-setuptools python3.12-venv python3.12-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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpcsclite1 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 media-types mummer netbase openjdk-21-jre-headless openssl perl perl-modules-5.40 python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools smalt 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After this operation, 495 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libsigsegv2 amd64 2.14-1+b2 [34.4 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:16 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:25 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get:35 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.106-1 [1392 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB] Get:41 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 fastaq all 3.17.0-9 [47.8 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:66 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:69 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 kmc amd64 3.2.4+dfsg-1+b1 [1049 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libbambamc0 amd64 0.0.50-6+b2 [38.2 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 smalt amd64 0.7.6-13 [115 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 iva amd64 1.0.11+ds-6 [8582 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 1s (192 MB/s) Selecting previously unselected package libmpfr6: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 ... 5142 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.2.1-1+b2_amd64.deb ... Unpacking libmpfr6:amd64 (4.2.1-1+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-5_amd64.deb ... 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 (8.2-5) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b2) ... Setting up libmpfr6:amd64 (4.2.1-1+b2) ... Setting up readline-common (8.2-5) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libsigsegv2:amd64 (2.14-1+b2) ... Selecting previously unselected package gawk. (Reading database ... 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Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../12-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... 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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 ... 6233 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... 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Unpacking smalt (0.7.6-13) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../50-libblas3_3.12.0-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../51-libgfortran5_14.2.0-8_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-8) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../52-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../53-python3-numpy_1%3a1.26.4+ds-12_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-12) ... Selecting previously unselected package iva. Preparing to unpack .../54-iva_1.0.11+ds-6_amd64.deb ... Unpacking iva (1.0.11+ds-6) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up java-common (0.76) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libblas3:amd64 (3.12.0-4) ... 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 (1:2.1.5-3+b1) ... Setting up libnspr4:amd64 (2:4.36-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up libbambamc0:amd64 (0.0.50-6+b2) ... Setting up libpcsclite1:amd64 (2.3.0-3) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up openssl (3.3.2-2) ... Setting up kmc (3.2.4+dfsg-1+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up smalt (0.7.6-13) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 libnss3:amd64 (2:3.106-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up mummer (3.23+dfsg-8) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up fastaq (3.17.0-9) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Processing triggers for libc-bin (2.40-4) ... 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 (2:1.21-76) ... Setting up iva (1.0.11+ds-6) ... 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. 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-6'] 0m27.2s INFO: Running scripts post_install 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_install_exceptions'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_install_exceptions'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_install_log_alternatives'] 0m27.2s 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-6: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=gawk: piuparts=iva=1.0.11+ds-6: /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-6: /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-6: /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-6: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=openjdk-21-jre-headless: piuparts=iva=1.0.11+ds-6: /usr/bin/update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-21-openjdk-amd64/bin/java 2111 --slave /usr/share/man/man1/java.1.gz java.1.gz /usr/lib/jvm/java-21-openjdk-amd64/man/man1/java.1.gz LOG-ALTERNATIVES: dpkg=openjdk-21-jre-headless: piuparts=iva=1.0.11+ds-6: /usr/bin/update-alternatives --install /usr/bin/jpackage jpackage /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage 2111 --slave /usr/share/man/man1/jpackage.1.gz jpackage.1.gz /usr/lib/jvm/java-21-openjdk-amd64/man/man1/jpackage.1.gz LOG-ALTERNATIVES: dpkg=openjdk-21-jre-headless: piuparts=iva=1.0.11+ds-6: /usr/bin/update-alternatives --install /usr/bin/keytool keytool /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool 2111 --slave /usr/share/man/man1/keytool.1.gz keytool.1.gz /usr/lib/jvm/java-21-openjdk-amd64/man/man1/keytool.1.gz LOG-ALTERNATIVES: dpkg=openjdk-21-jre-headless: piuparts=iva=1.0.11+ds-6: /usr/bin/update-alternatives --install /usr/bin/rmiregistry rmiregistry /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry 2111 --slave /usr/share/man/man1/rmiregistry.1.gz rmiregistry.1.gz /usr/lib/jvm/java-21-openjdk-amd64/man/man1/rmiregistry.1.gz LOG-ALTERNATIVES: dpkg=openjdk-21-jre-headless: piuparts=iva=1.0.11+ds-6: /usr/bin/update-alternatives --install /usr/bin/jexec jexec /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec 2111 --slave /usr/share/binfmts/jar jexec-binfmt /usr/lib/jvm/java-21-openjdk-amd64/lib/jar.binfmt 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_install_log_alternatives'] 0m27.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m28.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m29.5s ERROR: WARN: Broken symlinks: /usr/share/doc/python3-networkx/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js (python3-networkx) 0m30.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps483aocy', '-ac', '--ignore-obsolete'] 0m32.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps483aocy', '-ac', '--ignore-obsolete'] 0m32.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.3s DUMP: 0.15.6 0m32.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.3s INFO: Running adequate version 0.15.6 now. 0m32.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'iva'] 0m32.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'iva'] 0m32.5s INFO: Running scripts pre_remove 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/pre_remove_exceptions'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m34.2s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed fastaq fastaq 3.17.0-9 install ok installed findutils findutils 4.10.0-3 install ok installed gawk gawk 1:5.2.1-2+b1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed iva iva 1.0.11+ds-6 install ok installed java-common java-common 0.76 install ok installed kmc kmc 3.2.4+dfsg-1+b1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.16 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-6+b2 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.0-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-4 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b2 install ok installed libncurses6:amd64 libncurses6 6.5-2+b1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.6.0-2 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.9.1-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.9.1-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libnspr4:amd64 libnspr4 2:4.36-1 install ok installed libnss3:amd64 libnss3 2:3.106-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.0-3 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.8-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.8-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-12 install ok installed mummer mummer 3.23+dfsg-8 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.5+11-1 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed python3 python3 3.12.6-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-networkx python3-networkx 3.2.1-5 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-12 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pkg-resources python3-pkg-resources 75.2.0-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b2 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.12 python3.12 3.12.8-1 install ok installed python3.12-minimal python3.12-minimal 3.12.8-1 install ok installed readline-common readline-common 8.2-5 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed smalt smalt 0.7.6-13 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', '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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-21-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'smalt', 'iva'] 0m37.0s 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpcsclite1 libperl5.40 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1t64 libtirpc-common libtirpc3t64 media-types mummer netbase openjdk-21-jre-headless openssl perl perl-modules-5.40 python3 python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools smalt 0 upgraded, 0 newly installed, 79 to remove and 0 not upgraded. After this operation, 495 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 ... 14368 files and directories currently installed.) Removing iva (1.0.11+ds-6) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing fastaq (3.17.0-9) ... 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 (0.76) ... Removing kmc (3.2.4+dfsg-1+b1) ... Removing smalt (0.7.6-13) ... Removing libbambamc0:amd64 (0.0.50-6+b2) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing samtools (1.20-3) ... Removing python3-pysam (0.22.1+ds-2+b2) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.11.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libdeflate0:amd64 (1.22-1) ... Removing python3-networkx (3.2.1-5) ... Removing python3-pkg-resources (75.2.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing libmpfr6:amd64 (4.2.1-1+b2) ... Removing libncurses6:amd64 (6.5-2+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.6.0-2) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Removing libngtcp2-16:amd64 (1.9.1-1) ... Removing libnss3:amd64 (2:3.106-1) ... Removing libnspr4:amd64 (2:4.36-1) ... Removing libpcsclite1:amd64 (2.3.0-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libsigsegv2:amd64 (2.14-1+b2) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing openssl (3.3.2-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.8-1) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.8-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.8-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... 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 libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-4) ... 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', '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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-21-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'smalt', 'iva'] 0m37.0s INFO: Running scripts post_remove 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_remove_exceptions'] 0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_remove_exceptions'] 0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', '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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-21-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'smalt'] 0m37.2s DUMP: (Reading database ... 5194 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 (0.76) ... 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 (1.21.3-3) ... 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 libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 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 libperl5.40 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 libpython3.12-minimal:amd64 (3.12.8-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... 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 libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... 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-21-jre-headless:amd64 (21.0.5+11-1) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for python3 (3.12.6-1) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools 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-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.8-1) ... Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', '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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-21-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.40', 'python3', 'python3-autocommand', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'smalt'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--purge', 'iva'] 0m37.2s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--purge', 'iva'] 0m37.2s INFO: Running scripts post_purge 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_purge_exceptions'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_purge_exceptions'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--purge', '--pending'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--purge', '--pending'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--remove', '--pending'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg', '--remove', '--pending'] 0m37.3s INFO: Running scripts post_test 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_test_exceptions'] 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'tmp/scripts/post_test_exceptions'] 0m37.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m37.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m38.1s DEBUG: No broken symlinks as far as we can find. 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-divert', '--list'] 0m38.1s 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 /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 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 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 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'dpkg-divert', '--list'] 0m38.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'clean'] 0m38.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps483aocy', 'apt-get', 'clean'] 0m38.1s DEBUG: Recording chroot state 0m38.6s INFO: PASS: Installation and purging test. 0m38.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/shm'] 0m38.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/shm'] 0m38.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/console'] 0m38.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/console'] 0m38.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/ptmx'] 0m38.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/ptmx'] 0m38.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/pts'] 0m38.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/dev/pts'] 0m38.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/proc'] 0m39.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps483aocy/proc'] 0m39.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m39.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps483aocy'] 0m39.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmps483aocy 0m39.1s INFO: PASS: All tests. 0m39.1s INFO: piuparts run ends. ret=0 End: 2024-12-10 03:29:50 GMT