Start: 2024-11-09 21:08:34 GMT [testing] Package: phyml Source: phyml (3:3.3.20220408-3) Version: 3:3.3.20220408-3+b1 Installed-Size: 4432 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3t64 (>= 4.1.6), openmpi-bin Description: Phylogenetic estimation using Maximum Likelihood Homepage: http://www.atgc-montpellier.fr/phyml Description-md5: e17d56691eaa63bb88fc849229a6c8a4 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/p/phyml/phyml_3.3.20220408-3+b1_amd64.deb Size: 1104964 MD5sum: c1bd75bee9f196e84cf61ddcc56e589f SHA256: bf5b10ab1b7324121c8e1bd94e3b3ef6b7e81cf60d05d6479ef05abc3a81e395 [sid] Package: phyml Version: 3:3.3.20220408-4 Installed-Size: 4459 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3t64 (>= 5.0.5), mpi-default-bin Description: Phylogenetic estimation using Maximum Likelihood Homepage: http://www.atgc-montpellier.fr/phyml Description-md5: e17d56691eaa63bb88fc849229a6c8a4 Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/p/phyml/phyml_3.3.20220408-4_amd64.deb Size: 1105504 MD5sum: 5bc49d494ff5b8eeeecaec21d525a59a SHA256: 96490d9f440012f6536924c0e05b6f0dd9274b4f8234c2bf756cde0ea23e0e7e Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt phyml=3:3.3.20220408-4 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt phyml=3:3.3.20220408-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpuv6d6llo 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpuv6d6llo 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpuv6d6llo/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9344 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6241 kB] Fetched 15.8 MB in 1s (16.3 MB/s) Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: gcc-14-base libaudit-common libaudit1 libgcc-s1 libstdc++6 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 901 kB of archives. After this operation, 18.4 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:4.0.1-3 [12.4 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:4.0.1-3 [54.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 901 kB in 0s (13.1 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 ... 5167 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14.2.0-8_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up gcc-14-base:amd64 (14.2.0-8) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-8_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up libstdc++6:amd64 (14.2.0-8) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-8_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up libgcc-s1:amd64 (14.2.0-8) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.0.1-3_all.deb ... Unpacking libaudit-common (1:4.0.1-3) over (1:3.1.2-4) ... Setting up libaudit-common (1:4.0.1-3) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.1-3_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.1-3) over (1:3.1.2-4+b1) ... Setting up libaudit1:amd64 (1:4.0.1-3) ... Processing triggers for libc-bin (2.40-3) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 37c4b1fe6196420d8353990e4ec5f8d7 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m3.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m3.2s INFO: Running scripts is_testable 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s INFO: Running scripts pre_test 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_test_root_password'] 0m3.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_test_root_password'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m3.3s DUMP: Package: phyml Source: phyml (3:3.3.20220408-3) Version: 3:3.3.20220408-3+b1 Installed-Size: 4432 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3t64 (>= 4.1.6), openmpi-bin Description-en: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the ??comfort zone?? for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. . This package also includes PhyTime. Description-md5: e17d56691eaa63bb88fc849229a6c8a4 Homepage: http://www.atgc-montpellier.fr/phyml Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/p/phyml/phyml_3.3.20220408-3+b1_amd64.deb Size: 1104964 MD5sum: c1bd75bee9f196e84cf61ddcc56e589f SHA256: bf5b10ab1b7324121c8e1bd94e3b3ef6b7e81cf60d05d6479ef05abc3a81e395 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m3.3s INFO: apt-cache knows about the following packages: phyml 0m3.3s INFO: Running scripts pre_install 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m3.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m3.4s DUMP: phyml: Installed: (none) Candidate: 3:3.3.20220408-3+b1 Version table: 3:3.3.20220408-3+b1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml'] 0m8.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libcbor0.10 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.40 Suggested packages: liblocale-gettext-perl cron quota gdbm-l10n krb5-doc krb5-user libhwloc-contrib-plugins pciutils sensible-utils opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl Recommended packages: krb5-locales xauth netbase The following NEW packages will be installed: adduser ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libcbor0.10 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.40 phyml 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 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[43.4 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.3-2+b1 [662 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 phyml amd64 3:3.3.20220408-3+b1 [1105 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.2 MB in 1s (70.8 MB/s) Selecting previously unselected package perl-modules-5.40. 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Preparing to unpack .../42-ocl-icd-libopencl1_2.3.2-1+b2_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../43-libhwloc15_2.11.2-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.11.2-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../44-libhwloc-plugins_2.11.2-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... Selecting previously unselected package libibumad3:amd64. Preparing to unpack .../45-libibumad3_52.0-2+b1_amd64.deb ... Unpacking libibumad3:amd64 (52.0-2+b1) ... Selecting previously unselected package libibmad5:amd64. Preparing to unpack .../46-libibmad5_52.0-2+b1_amd64.deb ... Unpacking libibmad5:amd64 (52.0-2+b1) ... Selecting previously unselected package libmunge2:amd64. Preparing to unpack .../47-libmunge2_0.5.15-4+b1_amd64.deb ... Unpacking libmunge2:amd64 (0.5.15-4+b1) ... 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Setting up libpciaccess0:amd64 (0.17-3+b2) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up libcbor0.10:amd64 (0.10.2-2) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libibumad3:amd64 (52.0-2+b1) ... Setting up libibmad5:amd64 (52.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up perl-modules-5.40 (5.40.0-6) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b2) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libfido2-1:amd64 (1.15.0-1+b1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up libperl5.40:amd64 (5.40.0-6) ... Setting up perl (5.40.0-6) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up libpmix2t64:amd64 (5.0.3-2+b1) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up libhsa-runtime64-1:amd64 (5.7.1-3) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20220408-3+b1) ... Processing triggers for libc-bin (2.40-3) ... 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml'] 0m8.2s INFO: Running scripts post_install 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m8.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m8.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpuv6d6llo to sid 0m8.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m8.5s INFO: Running scripts pre_distupgrade 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'update'] 0m10.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7333 kB] Fetched 17.6 MB in 2s (10.9 MB/s) Reading package lists... 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'update'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-yf', 'dist-upgrade'] 0m12.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: mpi-default-bin The following packages will be upgraded: bsdutils libblkid1 libdebconfclient0 libhsa-runtime64-1 libhsakmt1 libmount1 libopenmpi3t64 libperl5.40 libsmartcols1 libsystemd0 libudev1 libuuid1 libx11-6 libx11-data login mount openmpi-bin openmpi-common perl perl-base perl-modules-5.40 phyml tzdata util-linux 24 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 17.4 MB of archives. After this operation, 798 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-10 [105 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-7 [4324 kB] Get:3 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-7 [267 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-7 [1675 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-7 [3017 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-10 [35.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-10 [168 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-10 [199 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-10 [139 kB] Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-10 [1217 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-10 [154 kB] Get:12 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-10 [81.4 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc1-4 [446 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc1-4 [146 kB] Get:16 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libopenmpi3t64 amd64 5.0.5-3 [2007 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:22 http://deb.debian.org/debian sid/main amd64 openmpi-common all 5.0.5-3 [95.0 kB] Get:23 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 5.0.5-3 [168 kB] Get:24 http://deb.debian.org/debian sid/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get:25 http://deb.debian.org/debian sid/main amd64 phyml amd64 3:3.3.20220408-4 [1106 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.4 MB in 0s (100 MB/s) (Reading database ... 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Setting up libdebconfclient0:amd64 (0.273) ... (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 ... 8581 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc1-4_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc1-4) over (256.7-3) ... Setting up libsystemd0:amd64 (257~rc1-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8581 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc1-4_amd64.deb ... Unpacking libudev1:amd64 (257~rc1-4) over (256.7-3) ... Setting up libudev1:amd64 (257~rc1-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8581 files and directories currently installed.) Preparing to unpack .../0-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) over (2024a-4) ... Preparing to unpack .../1-libhsakmt1_6.1.2+ds-1_amd64.deb ... Unpacking libhsakmt1:amd64 (6.1.2+ds-1) over (5.7.0-1) ... Preparing to unpack .../2-libhsa-runtime64-1_6.1.2-2_amd64.deb ... Unpacking libhsa-runtime64-1:amd64 (6.1.2-2) over (5.7.1-3) ... Preparing to unpack .../3-libopenmpi3t64_5.0.5-3_amd64.deb ... Unpacking libopenmpi3t64:amd64 (5.0.5-3) over (4.1.6-13.3) ... Preparing to unpack .../4-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) over (2:1.8.7-1) ... Preparing to unpack .../5-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) over (2:1.8.7-1+b2) ... Preparing to unpack .../6-openmpi-common_5.0.5-3_all.deb ... Unpacking openmpi-common (5.0.5-3) over (4.1.6-13.3) ... Preparing to unpack .../7-openmpi-bin_5.0.5-3_amd64.deb ... Unpacking openmpi-bin (5.0.5-3) over (4.1.6-13.3) ... Selecting previously unselected package mpi-default-bin. Preparing to unpack .../8-mpi-default-bin_1.17_amd64.deb ... Unpacking mpi-default-bin (1.17) ... Preparing to unpack .../9-phyml_3%3a3.3.20220408-4_amd64.deb ... Unpacking phyml (3:3.3.20220408-4) over (3:3.3.20220408-3+b1) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Nov 9 21:08:47 UTC 2024. Universal Time is now: Sat Nov 9 21:08:47 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libx11-data (2:1.8.10-2) ... Setting up libopenmpi3t64:amd64 (5.0.5-3) ... Setting up mount (2.40.2-10) ... Setting up perl-modules-5.40 (5.40.0-7) ... Setting up openmpi-common (5.0.5-3) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up openmpi-bin (5.0.5-3) ... update-alternatives: warning: forcing reinstallation of alternative /usr/bin/mpirun.openmpi because link group mpirun is broken update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.openmpi.1.gz (of link group mpirun) doesn't exist Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up login (1:4.16.0-2+really2.40.2-10) ... Setting up mpi-default-bin (1.17) ... Setting up libperl5.40:amd64 (5.40.0-7) ... Setting up perl (5.40.0-7) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up phyml (3:3.3.20220408-4) ... Processing triggers for libc-bin (2.40-3) ... 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-yf', 'dist-upgrade'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.8s DUMP: ae7804f34054c8cd0bbabc6d42c999d0 - 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m13.0s DUMP: Package: phyml Version: 3:3.3.20220408-4 Installed-Size: 4459 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3t64 (>= 5.0.5), mpi-default-bin Description-en: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the ??comfort zone?? for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. . This package also includes PhyTime. Description-md5: e17d56691eaa63bb88fc849229a6c8a4 Homepage: http://www.atgc-montpellier.fr/phyml Tag: biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, use::analysing, use::comparing, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/p/phyml/phyml_3.3.20220408-4_amd64.deb Size: 1105504 MD5sum: 5bc49d494ff5b8eeeecaec21d525a59a SHA256: 96490d9f440012f6536924c0e05b6f0dd9274b4f8234c2bf756cde0ea23e0e7e 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m13.0s INFO: apt-cache knows about the following packages: phyml 0m13.0s INFO: Running scripts pre_install 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m13.0s 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: 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m13.0s DUMP: phyml: Installed: 3:3.3.20220408-4 Candidate: 3:3.3.20220408-4 Version table: *** 3:3.3.20220408-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml'] 0m13.3s DUMP: Reading package lists... Building dependency tree... Reading state information... phyml is already the newest version (3:3.3.20220408-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml'] 0m13.3s INFO: Running scripts post_install 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m13.3s INFO: Running scripts post_distupgrade 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m13.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m13.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m14.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m14.0s INFO: Running scripts pre_install 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_database-server'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_exceptions'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_extras'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m14.0s 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: 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m14.1s DUMP: phyml: Installed: 3:3.3.20220408-4 Candidate: 3:3.3.20220408-4 Version table: *** 3:3.3.20220408-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-cache', 'policy', 'phyml'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml=3:3.3.20220408-4'] 0m14.3s DUMP: Reading package lists... Building dependency tree... Reading state information... phyml is already the newest version (3:3.3.20220408-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', '-y', 'install', 'phyml=3:3.3.20220408-4'] 0m14.3s INFO: Running scripts post_install 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_install_exceptions'] 0m14.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m14.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m14.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', '-ac', '--ignore-obsolete'] 0m15.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', '-ac', '--ignore-obsolete'] 0m15.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.9s DUMP: 0.15.6 0m15.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.9s INFO: Running adequate version 0.15.6 now. 0m15.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'phyml'] 0m16.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'phyml'] 0m16.0s INFO: Running scripts pre_remove 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.9s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_exceptions'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/pre_remove_exceptions'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.0s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-10 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed ibverbs-providers:amd64 ibverbs-providers 52.0-2+b1 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2 install ok installed libamdhip64-5 libamdhip64-5 5.7.1-5 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-10 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcbor0.10:amd64 libcbor0.10 0.10.2-2 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.123-1 install ok installed libdrm-common libdrm-common 2.4.123-1 install ok installed libdrm2:amd64 libdrm2 2.4.123-1 install ok installed libedit2:amd64 libedit2 3.1-20240808-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3.1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfido2-1:amd64 libfido2-1 1.15.0-1+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 6.1.2-2 install ok installed libhsakmt1:amd64 libhsakmt1 6.1.2+ds-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.11.2-1 install ok installed libhwloc15:amd64 libhwloc15 2.11.2-1 install ok installed libibmad5:amd64 libibmad5 52.0-2+b1 install ok installed libibumad3:amd64 libibumad3 52.0-2+b1 install ok installed libibverbs1:amd64 libibverbs1 52.0-2+b1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-18 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-10 install ok installed libmunge2:amd64 libmunge2 0.5.15-4+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.3+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.3+b1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenmpi3t64:amd64 libopenmpi3t64 5.0.5-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-7 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.3-2+b1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3 install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1 install ok installed librdmacm1t64:amd64 librdmacm1t64 52.0-2+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-10 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc1-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libucx0:amd64 libucx0 1.17.0+ds-3 install ok installed libudev1:amd64 libudev1 257~rc1-4 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-10 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.1 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-10 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-10 install ok installed mpi-default-bin mpi-default-bin 1.17 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1+b2 install ok installed openmpi-bin openmpi-bin 5.0.5-3 install ok installed openmpi-common openmpi-common 5.0.5-3 install ok installed openssh-client openssh-client 1:9.9p1-3 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.40.0-7 install ok installed perl-base perl-base 5.40.0-7 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-7 install ok installed phyml phyml 3:3.3.20220408-4 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-10 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'mpi-default-bin', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'perl', 'perl-modules-5.40', 'phyml'] 0m17.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libcbor0.10 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client perl perl-modules-5.40 phyml 0 upgraded, 0 newly installed, 61 to remove and 0 not upgraded. After this operation, 376 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 ... 8459 files and directories currently installed.) Removing phyml (3:3.3.20220408-4) ... Removing mpi-default-bin (1.17) ... Removing openmpi-bin (5.0.5-3) ... Removing libopenmpi3t64:amd64 (5.0.5-3) ... Removing libucx0:amd64 (1.17.0+ds-3) ... Removing libfabric1:amd64 (1.17.0-3.1) ... Removing librdmacm1t64:amd64 (52.0-2+b1) ... Removing openssh-client (1:9.9p1-3) ... Removing ibverbs-providers:amd64 (52.0-2+b1) ... Removing libamdhip64-5 (5.7.1-5) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libfido2-1:amd64 (1.15.0-1+b1) ... Removing libcbor0.10:amd64 (0.10.2-2) ... Removing libhsa-runtime64-1:amd64 (6.1.2-2) ... Removing libhsakmt1:amd64 (6.1.2+ds-1) ... Removing libdrm-amdgpu1:amd64 (2.4.123-1) ... Removing libdrm2:amd64 (2.4.123-1) ... Removing libdrm-common (2.4.123-1) ... Removing libllvm17t64:amd64 (1:17.0.6-18) ... Removing libedit2:amd64 (3.1-20240808-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libpmix2t64:amd64 (5.0.3-2+b1) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing perl (5.40.0-7) ... Removing libperl5.40:amd64 (5.40.0-7) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libhwloc-plugins:amd64 (2.11.2-1) ... Removing libhwloc15:amd64 (2.11.2-1) ... Removing libibmad5:amd64 (52.0-2+b1) ... Removing libibumad3:amd64 (52.0-2+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libmunge2:amd64 (0.5.15-4+b1) ... Removing libpsm2-2 (11.2.185-2.1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing libpciaccess0:amd64 (0.17-3+b2) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing libxnvctrl0:amd64 (535.171.04-1+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Removing openmpi-common (5.0.5-3) ... Removing perl-modules-5.40 (5.40.0-7) ... Removing libibverbs1:amd64 (52.0-2+b1) ... Removing adduser (3.137) ... Removing libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.3+b1) ... Processing triggers for libc-bin (2.40-3) ... 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'mpi-default-bin', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'perl', 'perl-modules-5.40', 'phyml'] 0m17.8s INFO: Running scripts post_remove 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_remove_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_remove_exceptions'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'mpi-default-bin', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'perl', 'perl-modules-5.40'] 0m17.8s DUMP: (Reading database ... 5194 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for ibverbs-providers:amd64 (52.0-2+b1) ... dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libcbor0.10 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libfido2-1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibmad5 which isn't installed dpkg: warning: ignoring request to remove libibumad3 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.3+b1) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenmpi3t64 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove mpi-default-bin which isn't installed dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openmpi-bin (5.0.5-3) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.9p1-3) ... Purging configuration files for perl (5.40.0-7) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'mpi-default-bin', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'perl', 'perl-modules-5.40'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', 'phyml'] 0m17.8s DUMP: dpkg: warning: ignoring request to remove phyml which isn't installed 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', 'phyml'] 0m17.8s INFO: Running scripts post_purge 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_purge_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_purge_exceptions'] 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', '--pending'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--purge', '--pending'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--remove', '--pending'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg', '--remove', '--pending'] 0m17.9s INFO: Running scripts post_test 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_test_exceptions'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'tmp/scripts/post_test_exceptions'] 0m17.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m18.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-divert', '--list'] 0m18.1s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'dpkg-divert', '--list'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'clean'] 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo', 'apt-get', 'clean'] 0m18.1s DEBUG: Recording chroot state 0m18.4s INFO: Warning: Package purging left files on system: /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 not owned 0m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/shm'] 0m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/shm'] 0m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/console'] 0m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/console'] 0m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/ptmx'] 0m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/ptmx'] 0m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts'] 0m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/dev/pts'] 0m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/proc'] 0m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo/proc'] 0m18.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m18.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpuv6d6llo'] 0m18.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpuv6d6llo 0m18.8s INFO: PASS: Upgrading between Debian distributions. 0m18.8s INFO: PASS: All tests. 0m18.8s INFO: piuparts run ends. ret=0 End: 2024-11-09 21:08:53 GMT