Start: 2025-08-12 06:55:36 GMT [trixie] Package: mauve-aligner Version: 2.4.0+4736-6 Installed-Size: 544 Maintainer: Debian Med Packaging Team Architecture: all Depends: libbiojava1.9-java, libcommons-cli-java, libdbus-java, libunixsocket-java, libzeus-jscl-java, java-wrappers, libbiojava-java (>= 1:1.9.5+dfsg-1), progressivemauve Description: multiple genome alignment Homepage: https://darlinglab.org/mauve/ Description-md5: 3a6b6e20614d8331f48ecec8afbd02a9 Section: science Priority: optional Filename: pool/main/m/mauve-aligner/mauve-aligner_2.4.0+4736-6_all.deb Size: 489224 MD5sum: f501782e59dfe8b906a5571b60393c64 SHA256: dc0950efad3a33efbd0d52d6aeda9b854ba0288d4d748306df8c6decac81b2c8 [trixie-next] Package: mauve-aligner Version: 2.4.0+4736-6 Installed-Size: 544 Maintainer: Debian Med Packaging Team Architecture: all Depends: libbiojava1.9-java, libcommons-cli-java, libdbus-java, libunixsocket-java, libzeus-jscl-java, java-wrappers, libbiojava-java (>= 1:1.9.5+dfsg-1), progressivemauve Description: multiple genome alignment Homepage: https://darlinglab.org/mauve/ Description-md5: 3a6b6e20614d8331f48ecec8afbd02a9 Section: science Priority: optional Filename: pool/main/m/mauve-aligner/mauve-aligner_2.4.0+4736-6_all.deb Size: 489224 MD5sum: f501782e59dfe8b906a5571b60393c64 SHA256: dc0950efad3a33efbd0d52d6aeda9b854ba0288d4d748306df8c6decac81b2c8 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt mauve-aligner=2.4.0+4736-6 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 1.6.1~202508101417~1.6.0-7-g17c4ea32 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt mauve-aligner=2.4.0+4736-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpiiv8u3i3 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpiiv8u3i3 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', '--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/tmpiiv8u3i3', '--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/tmpiiv8u3i3/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/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/tmpiiv8u3i3/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/tmpiiv8u3i3/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/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/tmpiiv8u3i3/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (11.4 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s INFO: Running scripts post_setup 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s 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 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m2.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m2.8s INFO: Running scripts is_testable 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s INFO: Running scripts pre_test 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_test_exceptions'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_test_exceptions'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_test_root_password'] 0m2.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_test_root_password'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'show', '--no-all-versions', 'mauve-aligner'] 0m2.9s DUMP: Package: mauve-aligner Version: 2.4.0+4736-6 Installed-Size: 544 Maintainer: Debian Med Packaging Team Architecture: all Depends: libbiojava1.9-java, libcommons-cli-java, libdbus-java, libunixsocket-java, libzeus-jscl-java, java-wrappers, libbiojava-java (>= 1:1.9.5+dfsg-1), progressivemauve Description-en: multiple genome alignment Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. . Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. . Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutition. . Mauve is developed at the University of Wisconsin. Description-md5: 3a6b6e20614d8331f48ecec8afbd02a9 Homepage: https://darlinglab.org/mauve/ Section: science Priority: optional Filename: pool/main/m/mauve-aligner/mauve-aligner_2.4.0+4736-6_all.deb Size: 489224 MD5sum: f501782e59dfe8b906a5571b60393c64 SHA256: dc0950efad3a33efbd0d52d6aeda9b854ba0288d4d748306df8c6decac81b2c8 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'show', '--no-all-versions', 'mauve-aligner'] 0m2.9s INFO: apt-cache knows about the following packages: mauve-aligner 0m2.9s INFO: Running scripts pre_install 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m2.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m3.0s DUMP: mauve-aligner: Installed: (none) Candidate: 2.4.0+4736-6 Version table: 2.4.0+4736-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner'] 0m4.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: java-wrappers libatinject-jsr330-api-java libbiojava-java libbiojava1.9-java libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libcommons-cli-java libcommons-dbcp-java libcommons-pool-java libdbus-java liberror-prone-java libgenome0 libgomp1 libguava-java libjgraph-java libjgrapht0.8-java libjsr305-java libmatthew-debug-java libmems1t64 libmuscle1 libunixsocket-java libzeus-jscl-java progressivemauve unzip Suggested packages: libatinject-jsr330-api-java-doc libgeronimo-jta-1.2-spec-java libjsr305-java-doc libmatthew-java-doc zip The following NEW packages will be installed: java-wrappers libatinject-jsr330-api-java libbiojava-java libbiojava1.9-java libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libcommons-cli-java libcommons-dbcp-java libcommons-pool-java libdbus-java liberror-prone-java libgenome0 libgomp1 libguava-java libjgraph-java libjgrapht0.8-java libjsr305-java libmatthew-debug-java libmems1t64 libmuscle1 libunixsocket-java libzeus-jscl-java mauve-aligner progressivemauve unzip 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 10.6 MB of archives. After this operation, 25.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-29 [173 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.5 [8848 B] Get:3 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get:4 http://deb.debian.org/debian trixie/main amd64 libcommons-pool-java all 1.6-5 [109 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libcommons-dbcp-java all 1.4-8 [157 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libjgraph-java all 5.12.4.2+dfsg-7 [207 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libjgrapht0.8-java all 0.8.3-7 [216 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libbiojava1.9-java all 1:1.9.7+dfsg-2 [3164 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libbiojava-java all 1:1.9.7+dfsg-2 [5552 B] Get:13 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.2 [282 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2 [254 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libmatthew-debug-java all 0.8.1-4 [12.8 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libunixsocket-java amd64 0.8.1-4 [15.1 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libdbus-java all 2.8-11 [141 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgenome0 amd64 1.3.11+svn20110227.4616-6+b2 [124 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libmuscle1 amd64 3.7+4565-8 [252 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libmems1t64 amd64 1.6.0+4725-11+b1 [702 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libzeus-jscl-java all 1.72-2 [129 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 progressivemauve amd64 1.2.0+4713+dfsg-5+b3 [871 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 mauve-aligner all 2.4.0+4736-6 [489 kB] Fetched 10.6 MB in 0s (39.0 MB/s) Selecting previously unselected package unzip. (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 ... 4938 files and directories currently installed.) Preparing to unpack .../00-unzip_6.0-29_amd64.deb ... Unpacking unzip (6.0-29) ... Selecting previously unselected package java-wrappers. Preparing to unpack .../01-java-wrappers_0.5_all.deb ... Unpacking java-wrappers (0.5) ... Selecting previously unselected package libatinject-jsr330-api-java. Preparing to unpack .../02-libatinject-jsr330-api-java_1.0+ds1-6_all.deb ... Unpacking libatinject-jsr330-api-java (1.0+ds1-6) ... Selecting previously unselected package libcommons-pool-java. Preparing to unpack .../03-libcommons-pool-java_1.6-5_all.deb ... Unpacking libcommons-pool-java (1.6-5) ... Selecting previously unselected package libcommons-dbcp-java. Preparing to unpack .../04-libcommons-dbcp-java_1.4-8_all.deb ... Unpacking libcommons-dbcp-java (1.4-8) ... Selecting previously unselected package liberror-prone-java. Preparing to unpack .../05-liberror-prone-java_2.18.0-1_all.deb ... Unpacking liberror-prone-java (2.18.0-1) ... Selecting previously unselected package libjsr305-java. Preparing to unpack .../06-libjsr305-java_0.1~+svn49-12_all.deb ... Unpacking libjsr305-java (0.1~+svn49-12) ... Selecting previously unselected package libguava-java. Preparing to unpack .../07-libguava-java_32.0.1-1_all.deb ... Unpacking libguava-java (32.0.1-1) ... Selecting previously unselected package libjgraph-java. Preparing to unpack .../08-libjgraph-java_5.12.4.2+dfsg-7_all.deb ... Unpacking libjgraph-java (5.12.4.2+dfsg-7) ... Selecting previously unselected package libjgrapht0.8-java. Preparing to unpack .../09-libjgrapht0.8-java_0.8.3-7_all.deb ... Unpacking libjgrapht0.8-java (0.8.3-7) ... Selecting previously unselected package libbiojava1.9-java. Preparing to unpack .../10-libbiojava1.9-java_1%3a1.9.7+dfsg-2_all.deb ... Unpacking libbiojava1.9-java (1:1.9.7+dfsg-2) ... Selecting previously unselected package libbiojava-java. Preparing to unpack .../11-libbiojava-java_1%3a1.9.7+dfsg-2_all.deb ... Unpacking libbiojava-java (1:1.9.7+dfsg-2) ... Selecting previously unselected package libboost-filesystem1.83.0:amd64. Preparing to unpack .../12-libboost-filesystem1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libboost-iostreams1.83.0:amd64. Preparing to unpack .../13-libboost-iostreams1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libboost-program-options1.83.0:amd64. Preparing to unpack .../14-libboost-program-options1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libcommons-cli-java. Preparing to unpack .../15-libcommons-cli-java_1.6.0-1_all.deb ... Unpacking libcommons-cli-java (1.6.0-1) ... Selecting previously unselected package libmatthew-debug-java. Preparing to unpack .../16-libmatthew-debug-java_0.8.1-4_all.deb ... Unpacking libmatthew-debug-java (0.8.1-4) ... Selecting previously unselected package libunixsocket-java. Preparing to unpack .../17-libunixsocket-java_0.8.1-4_amd64.deb ... Unpacking libunixsocket-java (0.8.1-4) ... Selecting previously unselected package libdbus-java. Preparing to unpack .../18-libdbus-java_2.8-11_all.deb ... Unpacking libdbus-java (2.8-11) ... Selecting previously unselected package libgenome0:amd64. Preparing to unpack .../19-libgenome0_1.3.11+svn20110227.4616-6+b2_amd64.deb ... Unpacking libgenome0:amd64 (1.3.11+svn20110227.4616-6+b2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../20-libgomp1_14.2.0-19_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-19) ... Selecting previously unselected package libmuscle1. Preparing to unpack .../21-libmuscle1_3.7+4565-8_amd64.deb ... Unpacking libmuscle1 (3.7+4565-8) ... Selecting previously unselected package libmems1t64:amd64. Preparing to unpack .../22-libmems1t64_1.6.0+4725-11+b1_amd64.deb ... Unpacking libmems1t64:amd64 (1.6.0+4725-11+b1) ... Selecting previously unselected package libzeus-jscl-java. Preparing to unpack .../23-libzeus-jscl-java_1.72-2_all.deb ... Unpacking libzeus-jscl-java (1.72-2) ... Selecting previously unselected package progressivemauve. Preparing to unpack .../24-progressivemauve_1.2.0+4713+dfsg-5+b3_amd64.deb ... Unpacking progressivemauve (1.2.0+4713+dfsg-5+b3) ... Selecting previously unselected package mauve-aligner. Preparing to unpack .../25-mauve-aligner_2.4.0+4736-6_all.deb ... Unpacking mauve-aligner (2.4.0+4736-6) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Setting up libjsr305-java (0.1~+svn49-12) ... Setting up libgenome0:amd64 (1.3.11+svn20110227.4616-6+b2) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up unzip (6.0-29) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libunixsocket-java (0.8.1-4) ... Setting up libmatthew-debug-java (0.8.1-4) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-6) ... Setting up libzeus-jscl-java (1.72-2) ... Setting up libcommons-pool-java (1.6-5) ... Setting up libdbus-java (2.8-11) ... Setting up libjgraph-java (5.12.4.2+dfsg-7) ... Setting up libcommons-dbcp-java (1.4-8) ... Setting up java-wrappers (0.5) ... Setting up libjgrapht0.8-java (0.8.3-7) ... Setting up libmuscle1 (3.7+4565-8) ... Setting up libmems1t64:amd64 (1.6.0+4725-11+b1) ... Setting up progressivemauve (1.2.0+4713+dfsg-5+b3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libbiojava1.9-java (1:1.9.7+dfsg-2) ... Setting up libbiojava-java (1:1.9.7+dfsg-2) ... Setting up mauve-aligner (2.4.0+4736-6) ... Processing triggers for libc-bin (2.41-12) ... 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner'] 0m4.2s INFO: Running scripts post_install 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m4.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpiiv8u3i3 to trixie-next 0m4.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m4.5s INFO: Running scripts pre_distupgrade 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'update'] 0m5.2s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:3 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:4 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:5 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:6 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:7 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Get:8 http://security.debian.org trixie-security InRelease [43.4 kB] Get:9 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:10 http://security.debian.org trixie-security/main Translation-en [6724 B] Fetched 172 kB in 0s (606 kB/s) Reading package lists... 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'update'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-yf', 'dist-upgrade'] 0m5.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-yf', 'dist-upgrade'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.7s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'show', '--no-all-versions', 'mauve-aligner'] 0m5.9s DUMP: Package: mauve-aligner Version: 2.4.0+4736-6 Installed-Size: 544 Maintainer: Debian Med Packaging Team Architecture: all Depends: libbiojava1.9-java, libcommons-cli-java, libdbus-java, libunixsocket-java, libzeus-jscl-java, java-wrappers, libbiojava-java (>= 1:1.9.5+dfsg-1), progressivemauve Description-en: multiple genome alignment Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. . Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. . Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutition. . Mauve is developed at the University of Wisconsin. Description-md5: 3a6b6e20614d8331f48ecec8afbd02a9 Homepage: https://darlinglab.org/mauve/ Section: science Priority: optional Filename: pool/main/m/mauve-aligner/mauve-aligner_2.4.0+4736-6_all.deb Size: 489224 MD5sum: f501782e59dfe8b906a5571b60393c64 SHA256: dc0950efad3a33efbd0d52d6aeda9b854ba0288d4d748306df8c6decac81b2c8 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'show', '--no-all-versions', 'mauve-aligner'] 0m5.9s INFO: apt-cache knows about the following packages: mauve-aligner 0m5.9s INFO: Running scripts pre_install 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m5.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m5.9s DUMP: mauve-aligner: Installed: 2.4.0+4736-6 Candidate: 2.4.0+4736-6 Version table: *** 2.4.0+4736-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner'] 0m6.2s DUMP: Reading package lists... Building dependency tree... Reading state information... mauve-aligner is already the newest version (2.4.0+4736-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner'] 0m6.2s INFO: Running scripts post_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m6.2s INFO: Running scripts post_distupgrade 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_zz_backports'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_distupgrade_zz_backports'] 0m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m6.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m6.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m6.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m6.6s INFO: Running scripts pre_install 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_database-server'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_exceptions'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_extras'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m6.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m6.7s DUMP: mauve-aligner: Installed: 2.4.0+4736-6 Candidate: 2.4.0+4736-6 Version table: *** 2.4.0+4736-6 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-cache', 'policy', 'mauve-aligner'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner=2.4.0+4736-6'] 0m6.9s DUMP: Reading package lists... Building dependency tree... Reading state information... mauve-aligner is already the newest version (2.4.0+4736-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', '-y', 'install', 'mauve-aligner=2.4.0+4736-6'] 0m6.9s INFO: Running scripts post_install 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_install_exceptions'] 0m6.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m7.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m7.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', '-ac', '--ignore-obsolete'] 0m7.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', '-ac', '--ignore-obsolete'] 0m7.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m7.7s DUMP: 0.15.9~deb12u1 0m7.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m7.7s INFO: Running adequate version 0.15.9~deb12u1 now. 0m7.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'mauve-aligner'] 0m7.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'mauve-aligner'] 0m7.7s INFO: Running scripts pre_remove 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/pre_remove_exceptions'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed java-wrappers java-wrappers 0.5 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-6 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libbiojava-java libbiojava-java 1:1.9.7+dfsg-2 install ok installed libbiojava1.9-java libbiojava1.9-java 1:1.9.7+dfsg-2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libboost-filesystem1.83.0:amd64 libboost-filesystem1.83.0 1.83.0-4.2 install ok installed libboost-iostreams1.83.0:amd64 libboost-iostreams1.83.0 1.83.0-4.2 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-4.2 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcommons-cli-java libcommons-cli-java 1.6.0-1 install ok installed libcommons-dbcp-java libcommons-dbcp-java 1.4-8 install ok installed libcommons-pool-java libcommons-pool-java 1.6-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdbus-java libdbus-java 2.8-11 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgenome0:amd64 libgenome0 1.3.11+svn20110227.4616-6+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libjgraph-java libjgraph-java 5.12.4.2+dfsg-7 install ok installed libjgrapht0.8-java libjgrapht0.8-java 0.8.3-7 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-12 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmatthew-debug-java libmatthew-debug-java 0.8.1-4 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmems1t64:amd64 libmems1t64 1.6.0+4725-11+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libmuscle1 libmuscle1 3.7+4565-8 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libunixsocket-java libunixsocket-java 0.8.1-4 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzeus-jscl-java libzeus-jscl-java 1.72-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mauve-aligner mauve-aligner 2.4.0+4736-6 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed progressivemauve progressivemauve 1.2.0+4713+dfsg-5+b3 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed unzip unzip 6.0-29 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'remove', '--allow-remove-essential', 'java-wrappers', 'libatinject-jsr330-api-java', 'libbiojava-java', 'libbiojava1.9-java', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libcommons-cli-java', 'libcommons-dbcp-java', 'libcommons-pool-java', 'libdbus-java', 'liberror-prone-java', 'libgenome0:amd64', 'libgomp1:amd64', 'libguava-java', 'libjgraph-java', 'libjgrapht0.8-java', 'libjsr305-java', 'libmatthew-debug-java', 'libmems1t64:amd64', 'libmuscle1', 'libunixsocket-java', 'libzeus-jscl-java', 'progressivemauve', 'unzip', 'mauve-aligner'] 0m8.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: java-wrappers libatinject-jsr330-api-java libbiojava-java libbiojava1.9-java libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libcommons-cli-java libcommons-dbcp-java libcommons-pool-java libdbus-java liberror-prone-java libgenome0 libgomp1 libguava-java libjgraph-java libjgrapht0.8-java libjsr305-java libmatthew-debug-java libmems1t64 libmuscle1 libunixsocket-java libzeus-jscl-java mauve-aligner progressivemauve unzip 0 upgraded, 0 newly installed, 26 to remove and 0 not upgraded. After this operation, 25.8 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 ... 5394 files and directories currently installed.) Removing mauve-aligner (2.4.0+4736-6) ... Removing java-wrappers (0.5) ... Removing libbiojava-java (1:1.9.7+dfsg-2) ... Removing libbiojava1.9-java (1:1.9.7+dfsg-2) ... Removing progressivemauve (1.2.0+4713+dfsg-5+b3) ... Removing libmems1t64:amd64 (1.6.0+4725-11+b1) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Removing libboost-iostreams1.83.0:amd64 (1.83.0-4.2) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Removing libcommons-cli-java (1.6.0-1) ... Removing libcommons-dbcp-java (1.4-8) ... Removing libcommons-pool-java (1.6-5) ... Removing libdbus-java (2.8-11) ... Removing libgenome0:amd64 (1.3.11+svn20110227.4616-6+b2) ... Removing libmuscle1 (3.7+4565-8) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libjgrapht0.8-java (0.8.3-7) ... Removing libjgraph-java (5.12.4.2+dfsg-7) ... Removing libmatthew-debug-java (0.8.1-4) ... Removing libunixsocket-java (0.8.1-4) ... Removing libzeus-jscl-java (1.72-2) ... Removing unzip (6.0-29) ... Removing libguava-java (32.0.1-1) ... Removing liberror-prone-java (2.18.0-1) ... Removing libatinject-jsr330-api-java (1.0+ds1-6) ... Removing libjsr305-java (0.1~+svn49-12) ... Processing triggers for libc-bin (2.41-12) ... 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'remove', '--allow-remove-essential', 'java-wrappers', 'libatinject-jsr330-api-java', 'libbiojava-java', 'libbiojava1.9-java', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libcommons-cli-java', 'libcommons-dbcp-java', 'libcommons-pool-java', 'libdbus-java', 'liberror-prone-java', 'libgenome0:amd64', 'libgomp1:amd64', 'libguava-java', 'libjgraph-java', 'libjgrapht0.8-java', 'libjsr305-java', 'libmatthew-debug-java', 'libmems1t64:amd64', 'libmuscle1', 'libunixsocket-java', 'libzeus-jscl-java', 'progressivemauve', 'unzip', 'mauve-aligner'] 0m8.5s INFO: Running scripts post_remove 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_remove_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_remove_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', 'java-wrappers', 'libatinject-jsr330-api-java', 'libbiojava-java', 'libbiojava1.9-java', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libcommons-cli-java', 'libcommons-dbcp-java', 'libcommons-pool-java', 'libdbus-java', 'liberror-prone-java', 'libgenome0:amd64', 'libgomp1:amd64', 'libguava-java', 'libjgraph-java', 'libjgrapht0.8-java', 'libjsr305-java', 'libmatthew-debug-java', 'libmems1t64:amd64', 'libmuscle1', 'libunixsocket-java', 'libzeus-jscl-java', 'progressivemauve', 'unzip'] 0m8.5s DUMP: dpkg: warning: ignoring request to remove java-wrappers which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java which isn't installed dpkg: warning: ignoring request to remove libbiojava-java which isn't installed dpkg: warning: ignoring request to remove libbiojava1.9-java which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libcommons-cli-java which isn't installed dpkg: warning: ignoring request to remove libcommons-dbcp-java which isn't installed dpkg: warning: ignoring request to remove libcommons-pool-java which isn't installed dpkg: warning: ignoring request to remove libdbus-java which isn't installed dpkg: warning: ignoring request to remove liberror-prone-java which isn't installed dpkg: warning: ignoring request to remove libgenome0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libguava-java which isn't installed dpkg: warning: ignoring request to remove libjgraph-java which isn't installed dpkg: warning: ignoring request to remove libjgrapht0.8-java which isn't installed dpkg: warning: ignoring request to remove libjsr305-java which isn't installed dpkg: warning: ignoring request to remove libmatthew-debug-java which isn't installed dpkg: warning: ignoring request to remove libmems1t64 which isn't installed dpkg: warning: ignoring request to remove libmuscle1 which isn't installed dpkg: warning: ignoring request to remove libunixsocket-java which isn't installed dpkg: warning: ignoring request to remove libzeus-jscl-java which isn't installed dpkg: warning: ignoring request to remove progressivemauve which isn't installed dpkg: warning: ignoring request to remove unzip which isn't installed 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', 'java-wrappers', 'libatinject-jsr330-api-java', 'libbiojava-java', 'libbiojava1.9-java', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libcommons-cli-java', 'libcommons-dbcp-java', 'libcommons-pool-java', 'libdbus-java', 'liberror-prone-java', 'libgenome0:amd64', 'libgomp1:amd64', 'libguava-java', 'libjgraph-java', 'libjgrapht0.8-java', 'libjsr305-java', 'libmatthew-debug-java', 'libmems1t64:amd64', 'libmuscle1', 'libunixsocket-java', 'libzeus-jscl-java', 'progressivemauve', 'unzip'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', 'mauve-aligner'] 0m8.5s DUMP: dpkg: warning: ignoring request to remove mauve-aligner which isn't installed 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', 'mauve-aligner'] 0m8.5s INFO: Running scripts post_purge 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_purge_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_purge_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', '--pending'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--purge', '--pending'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--remove', '--pending'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg', '--remove', '--pending'] 0m8.5s INFO: Running scripts post_test 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_test_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'tmp/scripts/post_test_exceptions'] 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-divert', '--list'] 0m8.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'dpkg-divert', '--list'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'clean'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3', 'apt-get', 'clean'] 0m8.8s DEBUG: Recording chroot state 0m9.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/shm'] 0m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/shm'] 0m9.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/console'] 0m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/console'] 0m9.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/ptmx'] 0m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/ptmx'] 0m9.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/pts'] 0m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/dev/pts'] 0m9.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/proc'] 0m9.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3/proc'] 0m9.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m9.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpiiv8u3i3'] 0m9.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpiiv8u3i3 0m9.5s INFO: PASS: Upgrading between Debian distributions. 0m9.5s INFO: PASS: All tests. 0m9.5s INFO: piuparts run ends. ret=0 End: 2025-08-12 06:55:46 GMT