Start: 2025-08-11 08:03:32 GMT [trixie] Package: mummer Version: 3.23+dfsg-8 Installed-Size: 3307 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), perl:any, gawk Description: Efficient sequence alignment of full genomes Homepage: https://mummer.sourceforge.net/ Description-md5: 38971f03178291c551b90e00bbe5418f Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, scope::utility, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/m/mummer/mummer_3.23+dfsg-8_amd64.deb Size: 661672 MD5sum: 04af4d909a3cdf81103b7fb7e2e2bf26 SHA256: 9d5f8f461331562e6c58f11a37f227c3334918d2f0c5e22e7715d21b7de85d2e [trixie-next] Package: mummer Version: 3.23+dfsg-8 Installed-Size: 3307 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), perl:any, gawk Description: Efficient sequence alignment of full genomes Homepage: https://mummer.sourceforge.net/ Description-md5: 38971f03178291c551b90e00bbe5418f Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, scope::utility, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/m/mummer/mummer_3.23+dfsg-8_amd64.deb Size: 661672 MD5sum: 04af4d909a3cdf81103b7fb7e2e2bf26 SHA256: 9d5f8f461331562e6c58f11a37f227c3334918d2f0c5e22e7715d21b7de85d2e 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 mummer=3.23+dfsg-8 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 mummer=3.23+dfsg-8 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmpviehnwde 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpviehnwde 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpviehnwde', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpviehnwde', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpviehnwde/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpviehnwde/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpviehnwde/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'update'] 0m2.5s 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 (8929 kB/s) Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-yf', 'dist-upgrade'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_dummy_users'] 0m4.5s 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 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_dummy_users'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s 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' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s 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 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m4.9s INFO: Running scripts is_testable 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s INFO: Running scripts pre_test 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m5.2s DUMP: Package: mummer Version: 3.23+dfsg-8 Installed-Size: 3307 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), perl:any, gawk Description-en: Efficient sequence alignment of full genomes MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. Description-md5: 38971f03178291c551b90e00bbe5418f Homepage: https://mummer.sourceforge.net/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, scope::utility, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/m/mummer/mummer_3.23+dfsg-8_amd64.deb Size: 661672 MD5sum: 04af4d909a3cdf81103b7fb7e2e2bf26 SHA256: 9d5f8f461331562e6c58f11a37f227c3334918d2f0c5e22e7715d21b7de85d2e 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m5.2s INFO: apt-cache knows about the following packages: mummer 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m5.3s 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: 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m5.3s DUMP: mummer: Installed: (none) Candidate: 3.23+dfsg-8 Version table: 3.23+dfsg-8 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer'] 0m7.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: gawk libgdbm-compat4t64 libgdbm6t64 libmpfr6 libperl5.40 libreadline8t64 libsigsegv2 perl perl-modules-5.40 readline-common Suggested packages: gawk-doc gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl readline-doc Recommended packages: netbase The following NEW packages will be installed: gawk libgdbm-compat4t64 libgdbm6t64 libmpfr6 libperl5.40 libreadline8t64 libsigsegv2 mummer perl perl-modules-5.40 readline-common 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 10.1 MB of archives. After this operation, 59.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [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 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.1-6 [267 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Fetched 10.1 MB in 0s (110 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 ... 4938 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.2.2-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.2.2-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-6_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 (8.2-6) ... 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 (4.2.2-1) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libsigsegv2:amd64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 4992 files and directories currently installed.) Preparing to unpack .../0-gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package perl-modules-5.40. Preparing to unpack .../1-perl-modules-5.40_5.40.1-6_all.deb ... Unpacking perl-modules-5.40 (5.40.1-6) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../2-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../3-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../4-libperl5.40_5.40.1-6_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.1-6) ... Selecting previously unselected package perl. Preparing to unpack .../5-perl_5.40.1-6_amd64.deb ... Unpacking perl (5.40.1-6) ... Selecting previously unselected package mummer. Preparing to unpack .../6-mummer_3.23+dfsg-8_amd64.deb ... Unpacking mummer (3.23+dfsg-8) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up perl (5.40.1-6) ... Setting up mummer (3.23+dfsg-8) ... Processing triggers for libc-bin (2.41-12) ... 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer'] 0m7.0s INFO: Running scripts post_install 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m7.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m7.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m7.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpviehnwde to trixie-next 0m7.4s 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 0m7.4s INFO: Running scripts pre_distupgrade 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'update'] 0m8.2s DUMP: Get:1 http://security.debian.org trixie-security InRelease [43.4 kB] Hit:2 http://deb.debian.org/debian trixie InRelease Get:3 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:4 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:5 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:6 http://security.debian.org trixie-security/main Translation-en [6724 B] Get:7 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:8 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:9 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:10 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Fetched 172 kB in 0s (1484 kB/s) Reading package lists... 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'update'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m9.9s DUMP: Package: mummer Version: 3.23+dfsg-8 Installed-Size: 3307 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), perl:any, gawk Description-en: Efficient sequence alignment of full genomes MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. Description-md5: 38971f03178291c551b90e00bbe5418f Homepage: https://mummer.sourceforge.net/ Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, scope::utility, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/m/mummer/mummer_3.23+dfsg-8_amd64.deb Size: 661672 MD5sum: 04af4d909a3cdf81103b7fb7e2e2bf26 SHA256: 9d5f8f461331562e6c58f11a37f227c3334918d2f0c5e22e7715d21b7de85d2e 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m9.9s INFO: apt-cache knows about the following packages: mummer 0m9.9s INFO: Running scripts pre_install 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m10.1s 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: 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m10.1s DUMP: mummer: Installed: 3.23+dfsg-8 Candidate: 3.23+dfsg-8 Version table: *** 3.23+dfsg-8 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer'] 0m10.6s DUMP: Reading package lists... Building dependency tree... Reading state information... mummer is already the newest version (3.23+dfsg-8). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer'] 0m10.6s INFO: Running scripts post_install 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m10.6s INFO: Running scripts post_distupgrade 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_zz_backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_distupgrade_zz_backports'] 0m10.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m10.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m11.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m11.3s INFO: Running scripts pre_install 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_database-server'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_exceptions'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_extras'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m11.4s 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: 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m11.4s DUMP: mummer: Installed: 3.23+dfsg-8 Candidate: 3.23+dfsg-8 Version table: *** 3.23+dfsg-8 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-cache', 'policy', 'mummer'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer=3.23+dfsg-8'] 0m12.0s DUMP: Reading package lists... Building dependency tree... Reading state information... mummer is already the newest version (3.23+dfsg-8). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', '-y', 'install', 'mummer=3.23+dfsg-8'] 0m12.0s INFO: Running scripts post_install 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_install_exceptions'] 0m12.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m12.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpviehnwde', '-ac', '--ignore-obsolete'] 0m14.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpviehnwde', '-ac', '--ignore-obsolete'] 0m14.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.0s DUMP: 0.15.9~deb12u1 0m14.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.0s INFO: Running adequate version 0.15.9~deb12u1 now. 0m14.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'mummer'] 0m14.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'mummer'] 0m14.5s INFO: Running scripts pre_remove 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_exceptions'] 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/pre_remove_exceptions'] 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m15.2s 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 gawk gawk 1:5.2.1-2+b1 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 libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 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 libmpfr6:amd64 libmpfr6 4.2.2-1 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 libperl5.40:amd64 libperl5.40 5.40.1-6 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 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 libsigsegv2:amd64 libsigsegv2 2.14-1+b2 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 mummer mummer 3.23+dfsg-8 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 perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed readline-common readline-common 8.2-6 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 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'remove', '--allow-remove-essential', 'gawk', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libmpfr6:amd64', 'libperl5.40:amd64', 'libreadline8t64:amd64', 'libsigsegv2:amd64', 'perl', 'perl-modules-5.40', 'readline-common', 'mummer'] 0m16.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gawk libgdbm-compat4t64 libgdbm6t64 libmpfr6 libperl5.40 libreadline8t64 libsigsegv2 mummer perl perl-modules-5.40 readline-common 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. After this operation, 59.8 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 ... 7433 files and directories currently installed.) 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 perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libmpfr6:amd64 (4.2.2-1) ... Removing libreadline8t64:amd64 (8.2-6) ... 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 libsigsegv2:amd64 (2.14-1+b2) ... Removing perl-modules-5.40 (5.40.1-6) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-12) ... 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'remove', '--allow-remove-essential', 'gawk', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libmpfr6:amd64', 'libperl5.40:amd64', 'libreadline8t64:amd64', 'libsigsegv2:amd64', 'perl', 'perl-modules-5.40', 'readline-common', 'mummer'] 0m16.2s INFO: Running scripts post_remove 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_remove_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_remove_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', 'gawk', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libmpfr6:amd64', 'libperl5.40:amd64', 'libreadline8t64:amd64', 'libsigsegv2:amd64', 'perl', 'perl-modules-5.40', 'readline-common'] 0m16.2s DUMP: (Reading database ... 4943 files and directories currently installed.) Purging configuration files for gawk (1:5.2.1-2+b1) ... 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 libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for readline-common (8.2-6) ... 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', 'gawk', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libmpfr6:amd64', 'libperl5.40:amd64', 'libreadline8t64:amd64', 'libsigsegv2:amd64', 'perl', 'perl-modules-5.40', 'readline-common'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', 'mummer'] 0m16.2s DUMP: dpkg: warning: ignoring request to remove mummer which isn't installed 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', 'mummer'] 0m16.2s INFO: Running scripts post_purge 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_purge_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_purge_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', '--pending'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--purge', '--pending'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--remove', '--pending'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg', '--remove', '--pending'] 0m16.2s INFO: Running scripts post_test 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_test_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'tmp/scripts/post_test_exceptions'] 0m16.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m16.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-divert', '--list'] 0m16.6s 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 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'dpkg-divert', '--list'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'clean'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpviehnwde', 'apt-get', 'clean'] 0m16.7s DEBUG: Recording chroot state 0m17.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/shm'] 0m17.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/shm'] 0m17.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/console'] 0m17.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/console'] 0m17.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/ptmx'] 0m17.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/ptmx'] 0m17.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts'] 0m17.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/dev/pts'] 0m17.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/proc'] 0m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpviehnwde/proc'] 0m17.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m17.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpviehnwde'] 0m17.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpviehnwde 0m17.8s INFO: PASS: Upgrading between Debian distributions. 0m17.8s INFO: PASS: All tests. 0m17.8s INFO: piuparts run ends. ret=0 End: 2025-08-11 08:03:50 GMT