Start: 2022-12-04 15:31:14 GMT [testing] Package: mummer Version: 3.23+dfsg-7 Installed-Size: 3321 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), perl:any, gawk Description: Efficient sequence alignment of full genomes Homepage: http://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-7_amd64.deb Size: 664260 MD5sum: 54425675719b8e0d7b9f1472a8816f8e SHA256: cd4eea0e066236bb0eaffe2573ca12ae65a100dd183ec807d6a3688faa1daf41 [sid] 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/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt mummer=3.23+dfsg-8 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmplidu61oq 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmplidu61oq 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmplidu61oq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmplidu61oq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmplidu61oq/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmplidu61oq/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/shm'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmplidu61oq/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'update'] 0m4.6s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [164 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8784 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5932 kB] Fetched 14.9 MB in 2s (7827 kB/s) Reading package lists... 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'update'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: debconf libc-bin libc6 libsystemd0 libudev1 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3904 kB of archives. After this operation, 21.5 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-6 [2745 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-6 [604 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.80 [121 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.2-1 [329 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.2-1 [106 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3904 kB in 0s (48.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8594 files and directories currently installed.) Preparing to unpack .../libc6_2.36-6_amd64.deb ... Unpacking libc6:amd64 (2.36-6) over (2.36-5) ... Setting up libc6:amd64 (2.36-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8594 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-6_amd64.deb ... Unpacking libc-bin (2.36-6) over (2.36-5) ... Setting up libc-bin (2.36-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8594 files and directories currently installed.) Preparing to unpack .../debconf_1.5.80_all.deb ... Unpacking debconf (1.5.80) over (1.5.79) ... Setting up debconf (1.5.80) ... (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 ... 8594 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.2-1_amd64.deb ... Unpacking libsystemd0:amd64 (252.2-1) over (252.1-1) ... Setting up libsystemd0:amd64 (252.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8594 files and directories currently installed.) Preparing to unpack .../libudev1_252.2-1_amd64.deb ... Unpacking libudev1:amd64 (252.2-1) over (252.1-1) ... Setting up libudev1:amd64 (252.2-1) ... Processing triggers for libc-bin (2.36-6) ... 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s DUMP: 7dd7a322ceb2eb537df9d7643133c36d - 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s INFO: Running scripts post_setup 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_dummy_users'] 0m7.7s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_dummy_users'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_forbid_home'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_minimize'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_zz_backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_setup_zz_backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.8s DUMP: install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.80 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9+b1 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-9 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-6 install ok installed libc6:amd64 libc6 2.36-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.265 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.8-0.0 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-2 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b3 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b3 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 252.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252.2-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m8.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m8.2s INFO: Running scripts is_testable 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s INFO: Running scripts pre_test 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_test_root_password'] 0m8.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_test_root_password'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m8.5s DUMP: Package: mummer Version: 3.23+dfsg-7 Installed-Size: 3321 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), 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: http://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-7_amd64.deb Size: 664260 MD5sum: 54425675719b8e0d7b9f1472a8816f8e SHA256: cd4eea0e066236bb0eaffe2573ca12ae65a100dd183ec807d6a3688faa1daf41 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m8.5s INFO: apt-cache knows about the following packages: mummer 0m8.5s INFO: Running scripts pre_install 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m8.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m8.6s DUMP: mummer: Installed: (none) Candidate: 3.23+dfsg-7 Version table: 3.23+dfsg-7 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer'] 0m9.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: gawk libmpfr6 libreadline8 libsigsegv2 readline-common Suggested packages: gawk-doc readline-doc The following NEW packages will be installed: gawk libmpfr6 libreadline8 libsigsegv2 mummer readline-common 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 3552 kB of archives. After this operation, 10.1 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.1.0-3 [2012 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.2 [68.5 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.2 [165 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 gawk amd64 1:5.1.0-1 [605 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3552 kB in 0s (56.0 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 ... 8596 files and directories currently installed.) Preparing to unpack .../libmpfr6_4.1.0-3_amd64.deb ... Unpacking libmpfr6:amd64 (4.1.0-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../readline-common_8.2-1.2_all.deb ... Unpacking readline-common (8.2-1.2) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../libreadline8_8.2-1.2_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1) ... Setting up libmpfr6:amd64 (4.1.0-3) ... Setting up readline-common (8.2-1.2) ... Setting up libreadline8:amd64 (8.2-1.2) ... Setting up libsigsegv2:amd64 (2.14-1) ... 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 ... 8640 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.1.0-1_amd64.deb ... Unpacking gawk (1:5.1.0-1) ... Selecting previously unselected package mummer. Preparing to unpack .../mummer_3.23+dfsg-7_amd64.deb ... Unpacking mummer (3.23+dfsg-7) ... Setting up gawk (1:5.1.0-1) ... Setting up mummer (3.23+dfsg-7) ... Processing triggers for libc-bin (2.36-6) ... 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer'] 0m9.5s INFO: Running scripts post_install 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m9.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m9.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m9.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmplidu61oq to sid 0m9.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.9s INFO: Running scripts pre_distupgrade 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'update'] 0m13.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [161 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9396 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6946 kB] Fetched 16.5 MB in 3s (5931 kB/s) Reading package lists... 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'update'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-yf', 'dist-upgrade'] 0m14.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libmd0 The following packages will be upgraded: dpkg libacl1 libattr1 liblzma5 libpcre2-8-0 mummer tar zlib1g 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 4507 kB of archives. After this operation, 109 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:2 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.1 [836 kB] Get:3 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.21.11 [2404 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.1-2 [25.2 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.1-2 [15.4 kB] Get:6 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.2.9-0.0 [189 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.40-3 [260 kB] Get:8 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4507 kB in 0s (75.9 MB/s) Selecting previously unselected package libmd0: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 ... 8903 files and directories currently installed.) Preparing to unpack .../libmd0_1.0.4-2_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-2) ... Setting up libmd0:amd64 (1.0.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8909 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.1_amd64.deb ... Unpacking tar (1.34+dfsg-1.1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8909 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.11_amd64.deb ... Unpacking dpkg (1.21.11) over (1.21.9+b1) ... Setting up dpkg (1.21.11) ... (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 ... 8907 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-2_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-2) over (2.3.1-1) ... Setting up libacl1:amd64 (2.3.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8908 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.1-2_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-2) over (1:2.5.1-1) ... Setting up libattr1:amd64 (1:2.5.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8909 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.9-0.0_amd64.deb ... Unpacking liblzma5:amd64 (5.2.9-0.0) over (5.2.8-0.0) ... Setting up liblzma5:amd64 (5.2.9-0.0) ... (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 ... 8909 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.40-3_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.40-3) over (10.40-2) ... Setting up libpcre2-8-0:amd64 (10.40-3) ... (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 ... 8909 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-4.1) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8909 files and directories currently installed.) Preparing to unpack .../mummer_3.23+dfsg-8_amd64.deb ... Unpacking mummer (3.23+dfsg-8) over (3.23+dfsg-7) ... Setting up mummer (3.23+dfsg-8) ... Processing triggers for libc-bin (2.36-6) ... 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-yf', 'dist-upgrade'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.4s DUMP: 3207d58a5071018c75aa7d837d9d39ff - 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m15.6s 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 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'show', '--no-all-versions', 'mummer'] 0m15.6s INFO: apt-cache knows about the following packages: mummer 0m15.6s INFO: Running scripts pre_install 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m15.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m15.8s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer'] 0m16.3s 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. 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer'] 0m16.3s INFO: Running scripts post_install 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m16.3s INFO: Running scripts post_distupgrade 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m16.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m16.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m17.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m17.3s INFO: Running scripts pre_install 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_database-server'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_exceptions'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_extras'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m17.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m17.6s 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 sid/main amd64 Packages 100 /var/lib/dpkg/status 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-cache', 'policy', 'mummer'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer=3.23+dfsg-8'] 0m18.0s 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. 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', '-y', 'install', 'mummer=3.23+dfsg-8'] 0m18.0s INFO: Running scripts post_install 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_install_exceptions'] 0m18.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m18.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m19.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmplidu61oq', '-ac', '--ignore-obsolete'] 0m20.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmplidu61oq', '-ac', '--ignore-obsolete'] 0m20.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.4s DUMP: 0.15.6 0m20.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.4s INFO: Running adequate version 0.15.6 now. 0m20.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'mummer'] 0m20.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'mummer'] 0m20.9s INFO: Running scripts pre_remove 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_exceptions'] 0m22.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/pre_remove_exceptions'] 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.5s DUMP: install ok installed apt apt 2.5.4 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.80 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.11 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed gawk gawk 1:5.1.0-1 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-9 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.4 install ok installed libattr1:amd64 libattr1 1:2.5.1-2 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-6 install ok installed libc6:amd64 libc6 2.36-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b2 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.265 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.9-0.0 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libmpfr6:amd64 libmpfr6 4.1.0-3 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-3 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libreadline8:amd64 libreadline8 8.2-1.2 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b2 install ok installed libselinux1:amd64 libselinux1 3.4-1+b3 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b3 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 252.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252.2-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed mummer mummer 3.23+dfsg-8 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed readline-common readline-common 8.2-1.2 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-7 install ok installed tar tar 1.34+dfsg-1.1 install ok installed tzdata tzdata 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'remove', 'gawk', 'libmpfr6:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'readline-common', 'mummer'] 0m23.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gawk libmpfr6 libreadline8 libsigsegv2 mummer readline-common 0 upgraded, 0 newly installed, 6 to remove and 0 not upgraded. After this operation, 10.0 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 ... 8909 files and directories currently installed.) Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.1.0-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libmpfr6:amd64 (4.1.0-3) ... Removing libreadline8:amd64 (8.2-1.2) ... Removing libsigsegv2:amd64 (2.14-1) ... Removing readline-common (8.2-1.2) ... Processing triggers for libc-bin (2.36-6) ... 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'remove', 'gawk', 'libmpfr6:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'readline-common', 'mummer'] 0m23.4s INFO: Running scripts post_remove 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_remove_exceptions'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_remove_exceptions'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', 'gawk', 'libmpfr6:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'readline-common'] 0m23.4s DUMP: (Reading database ... 8604 files and directories currently installed.) Purging configuration files for gawk (1:5.1.0-1) ... dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed Purging configuration files for readline-common (8.2-1.2) ... 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', 'gawk', 'libmpfr6:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'readline-common'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', 'mummer'] 0m23.5s DUMP: dpkg: warning: ignoring request to remove mummer which isn't installed 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', 'mummer'] 0m23.5s INFO: Running scripts post_purge 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_purge_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_purge_exceptions'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', '--pending'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--purge', '--pending'] 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--remove', '--pending'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg', '--remove', '--pending'] 0m23.5s INFO: Running scripts post_test 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_test_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'tmp/scripts/post_test_exceptions'] 0m23.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m24.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-divert', '--list'] 0m24.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'dpkg-divert', '--list'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'clean'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmplidu61oq', 'apt-get', 'clean'] 0m24.1s DEBUG: Recording chroot state 0m25.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/shm'] 0m25.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/shm'] 0m25.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/console'] 0m25.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/console'] 0m25.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/ptmx'] 0m25.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/ptmx'] 0m25.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts'] 0m25.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/dev/pts'] 0m25.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/proc'] 0m25.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmplidu61oq/proc'] 0m25.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m25.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmplidu61oq'] 0m25.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmplidu61oq 0m25.5s INFO: PASS: Upgrading between Debian distributions. 0m25.5s INFO: PASS: All tests. 0m25.5s INFO: piuparts run ends. ret=0 End: 2022-12-04 15:31:40 GMT