Start: 2024-12-05 03:27:01 GMT [testing] Package: iva Version: 1.0.11+ds-5 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-5_amd64.deb Size: 8581624 MD5sum: 81641314ba9e9e3b5e100a7443802397 SHA256: 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef [sid] 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 --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 testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --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 --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 testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt iva=1.0.11+ds-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmpoc3xoh4_ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpoc3xoh4_ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpoc3xoh4_/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'update'] 0m1.7s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9348 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6273 kB] Fetched 15.8 MB in 1s (16.0 MB/s) Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 libcap-ng0 libseccomp2 libsystemd0 libudev1 tzdata 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3426 kB of archives. After this operation, 31.7 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257~rc3-1 [448 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257~rc3-1 [147 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.16 [1113 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.16 [1397 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3426 kB in 0s (39.2 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 ... 5150 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc3-1_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libsystemd0:amd64 (257~rc3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5150 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc3-1_amd64.deb ... Unpacking libudev1:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libudev1:amd64 (257~rc3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5150 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.16_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.16) over (2.9.14) ... Setting up libapt-pkg6.0t64:amd64 (2.9.16) ... (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 ... 5150 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (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 ... 5149 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.16_amd64.deb ... Unpacking apt (2.9.16) over (2.9.14) ... Setting up apt (2.9.16) ... (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 ... 5149 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-4_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4) over (0.8.5-3+b1) ... Setting up libcap-ng0:amd64 (0.8.5-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) over (2024b-3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 5 03:27:03 UTC 2024. Universal Time is now: Thu Dec 5 03:27:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.40-3) ... 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s DUMP: a29e00c0a36a798deb0473312a502fd3 - 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s INFO: Running scripts post_setup 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s 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 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s 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' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s 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 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 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 1.47.1-1+b1 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 2.40.2-11 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 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 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 1.47.1-1+b1 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 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 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-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 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 2.40.2-11 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 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 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 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 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+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 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 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m3.9s INFO: Running scripts is_testable 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s INFO: Running scripts pre_test 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_test_root_password'] 0m3.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_test_root_password'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m4.0s DUMP: Package: iva Version: 1.0.11+ds-5 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-5_amd64.deb Size: 8581624 MD5sum: 81641314ba9e9e3b5e100a7443802397 SHA256: 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m4.0s INFO: apt-cache knows about the following packages: iva 0m4.0s INFO: Running scripts pre_install 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m4.1s 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: 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m4.1s DUMP: iva: Installed: (none) Candidate: 1.0.11+ds-5 Version table: 1.0.11+ds-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva'] 0m15.7s 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 3.12.7-3 [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 3.12.7-3 [2162 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 3.12.7-3 [1966 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 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 3.17.0-8 [47.7 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 74.1.2-2 [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-5 [8582 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 2s (58.1 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 ... 5152 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 ... 6241 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-5_amd64.deb ... Unpacking iva (1.0.11+ds-5) ... 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 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... 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 (3.17.0-8) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Processing triggers for libc-bin (2.40-3) ... 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-5) ... /usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') /usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) 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. 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva'] 0m15.7s INFO: Running scripts post_install 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m15.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m16.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m16.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpoc3xoh4_ to sid 0m16.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m16.2s INFO: Running scripts pre_distupgrade 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'update'] 0m18.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7346 kB] Fetched 17.6 MB in 2s (11.3 MB/s) Reading package lists... 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'update'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: e2fsprogs iva libc-bin libc6 libcom-err2 libdebconfclient0 libext2fs2t64 libgmp10 libgpg-error0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libss2 libunistring5 logsave python3 python3-minimal python3-pkg-resources python3.12 python3.12-minimal 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 MB of archives. After this operation, 350 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Get:3 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.2~rc1-2 [23.6 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.2~rc1-2 [211 kB] Get:5 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.2~rc1-2 [588 kB] Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get:10 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:13 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.274 [10.1 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.51-2 [82.1 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:17 http://deb.debian.org/debian sid/main amd64 iva amd64 1.0.11+ds-6 [8582 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.2~rc1-2 [28.4 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 MB in 0s (49.8 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 ... 14377 files and directories currently installed.) Preparing to unpack .../libc6_2.40-4_amd64.deb ... Unpacking libc6:amd64 (2.40-4) over (2.40-3) ... Setting up libc6:amd64 (2.40-4) ... (Reading database ... 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Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Unpacking libext2fs2t64:amd64 (1.47.2~rc1-2) over (1.47.1-1+b1) ... Setting up libext2fs2t64:amd64 (1.47.2~rc1-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14375 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 ... 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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 ... 14374 files and directories currently installed.) Preparing to unpack .../iva_1.0.11+ds-6_amd64.deb ... Unpacking iva (1.0.11+ds-6) over (1.0.11+ds-5) ... Preparing to unpack .../libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) over (1.47.1-1+b1) ... Preparing to unpack .../libss2_1.47.2~rc1-2_amd64.deb ... Unpacking libss2:amd64 (1.47.2~rc1-2) over (1.47.1-1+b1) ... Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-2) ... Setting up libpython3.12-minimal:amd64 (3.12.8-1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-2) ... Setting up libss2:amd64 (1.47.2~rc1-2) ... Setting up logsave (1.47.2~rc1-2) ... Setting up python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up e2fsprogs (1.47.2~rc1-2) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up iva (1.0.11+ds-6) ... Processing triggers for libc-bin (2.40-4) ... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.2s DUMP: 07b37819b34cdf1083ef43104857c8ba - 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m22.3s DUMP: 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-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva 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 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m22.3s INFO: apt-cache knows about the following packages: iva 0m22.3s INFO: Running scripts pre_install 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m22.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m22.4s DUMP: iva: Installed: 1.0.11+ds-6 Candidate: 1.0.11+ds-6 Version table: *** 1.0.11+ds-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva'] 0m22.7s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva'] 0m22.7s INFO: Running scripts post_install 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m22.7s INFO: Running scripts post_distupgrade 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m23.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m23.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m23.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m23.7s INFO: Running scripts pre_install 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_database-server'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_exceptions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_extras'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m23.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m23.7s DUMP: iva: Installed: 1.0.11+ds-6 Candidate: 1.0.11+ds-6 Version table: *** 1.0.11+ds-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-cache', 'policy', 'iva'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-6'] 0m24.0s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-6'] 0m24.0s INFO: Running scripts post_install 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_install_exceptions'] 0m24.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m24.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m25.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '-ac', '--ignore-obsolete'] 0m26.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '-ac', '--ignore-obsolete'] 0m26.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.4s DUMP: 0.15.6 0m26.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.4s INFO: Running adequate version 0.15.6 now. 0m26.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'iva'] 0m26.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'iva'] 0m26.4s INFO: Running scripts pre_remove 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/pre_remove_exceptions'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m27.4s 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 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 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 3.17.0-8 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 2.40.2-11 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 2.40.2-11 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 3.12.7-1 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 2.40.2-11 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 2.40.2-11 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+really2.40.2-11 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 2.40.2-11 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 3.12.7-1 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 3.12.7-1 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 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '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'] 0m29.0s 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 ... 14372 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 (3.17.0-8) ... 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 (3.12.7-1) ... Removing python3.12 (3.12.8-1) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.8-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... 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) ... 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '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'] 0m29.0s INFO: Running scripts post_remove 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_remove_exceptions'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_remove_exceptions'] 0m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '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'] 0m29.1s DUMP: (Reading database ... 5198 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 (3.12.7-1) ... 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 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', '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'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--purge', 'iva'] 0m29.1s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--purge', 'iva'] 0m29.1s INFO: Running scripts post_purge 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_purge_exceptions'] 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_purge_exceptions'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--purge', '--pending'] 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--purge', '--pending'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--remove', '--pending'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg', '--remove', '--pending'] 0m29.2s INFO: Running scripts post_test 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_test_exceptions'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'tmp/scripts/post_test_exceptions'] 0m29.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m29.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-divert', '--list'] 0m29.4s 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 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'dpkg-divert', '--list'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'clean'] 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_', 'apt-get', 'clean'] 0m29.4s DEBUG: Recording chroot state 0m29.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/shm'] 0m29.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/shm'] 0m29.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/console'] 0m29.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/console'] 0m29.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/ptmx'] 0m29.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/ptmx'] 0m29.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts'] 0m29.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/dev/pts'] 0m29.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/proc'] 0m29.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_/proc'] 0m29.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m30.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpoc3xoh4_'] 0m30.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpoc3xoh4_ 0m30.0s INFO: PASS: Upgrading between Debian distributions. 0m30.0s INFO: PASS: All tests. 0m30.0s INFO: piuparts run ends. ret=0 End: 2024-12-05 03:27:31 GMT