Start: 2024-08-21 18:28:17 GMT [bookworm] Package: phyml Version: 3:3.3.20220408-3 Installed-Size: 4419 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3 (>= 4.1.4), 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_amd64.deb Size: 1103096 MD5sum: 05c8e5cf027e5f15ae1718f8fdd4670f SHA256: 219c33f8814f714589718d2ac2b00f002674d193a3700f2e7cec75e54f7549d1 [bookworm-next] Package: phyml Version: 3:3.3.20220408-3 Installed-Size: 4419 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3 (>= 4.1.4), 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_amd64.deb Size: 1103096 MD5sum: 05c8e5cf027e5f15ae1718f8fdd4670f SHA256: 219c33f8814f714589718d2ac2b00f002674d193a3700f2e7cec75e54f7549d1 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt phyml=3:3.3.20220408-3 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 1.4.4~202408201135~1.4.3-10-g39df1906 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt phyml=3:3.3.20220408-3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnwn920bb 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnwn920bb 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnwn920bb/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'update'] 0m1.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 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 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s INFO: Running scripts pre_test 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m4.7s DUMP: Package: phyml Version: 3:3.3.20220408-3 Installed-Size: 4419 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3 (>= 4.1.4), 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_amd64.deb Size: 1103096 MD5sum: 05c8e5cf027e5f15ae1718f8fdd4670f SHA256: 219c33f8814f714589718d2ac2b00f002674d193a3700f2e7cec75e54f7549d1 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m4.7s INFO: apt-cache knows about the following packages: phyml 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m4.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m4.8s DUMP: phyml: Installed: (none) Candidate: 3:3.3.20220408-3 Version table: 3:3.3.20220408-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml'] 0m10.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ibverbs-providers libatomic1 libbsd0 libcbor0.8 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client Suggested packages: krb5-doc krb5-user libhwloc-contrib-plugins pciutils opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass Recommended packages: krb5-locales xauth The following NEW packages will be installed: ibverbs-providers libatomic1 libbsd0 libcbor0.8 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client phyml 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 22.9 MB of archives. After this operation, 84.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:9 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2+deb12u2 [990 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:17 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-3~deb12u1 [13.5 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+deb12u1 [622 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 phyml amd64 3:3.3.20220408-3 [1103 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.9 MB in 1s (21.2 MB/s) Selecting previously unselected package libbsd0: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 ... 6093 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../02-libcbor0.8_0.8.0-2+b1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2+b1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../03-libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../04-libfido2-1_1.12.0-2+b1_amd64.deb ... Unpacking libfido2-1:amd64 (1.12.0-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../05-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. 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Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../19-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../20-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../21-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../22-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../23-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../24-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... 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Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../37-libpmix2_4.2.2-1+deb12u1_amd64.deb ... Unpacking libpmix2:amd64 (4.2.2-1+deb12u1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../38-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../39-libopenmpi3_4.1.4-3+b1_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.4-3+b1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../40-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../41-openmpi-bin_4.1.4-3+b1_amd64.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package phyml. Preparing to unpack .../42-phyml_3%3a3.3.20220408-3_amd64.deb ... Unpacking phyml (3:3.3.20220408-3) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libicu72:amd64 (72.1-3) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libssl3:amd64 (3.0.13-1~deb12u1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 (1.12.0-2+b1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2+deb12u2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1+deb12u1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml'] 0m10.7s INFO: Running scripts post_install 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m10.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m11.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m11.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpnwn920bb to bookworm-next 0m11.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m11.3s INFO: Running scripts pre_distupgrade 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'update'] 0m13.2s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [90.8 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [51.3 kB] Fetched 616 kB in 1s (635 kB/s) Reading package lists... 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'update'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-yf', 'dist-upgrade'] 0m16.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 openssh-client 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7395 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:2 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://security.debian.org bookworm-security/main amd64 openssh-client amd64 1:9.2p1-2+deb12u3 [991 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7395 kB in 0s (52.0 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 ... 7181 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 7181 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (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 ... 7181 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (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 ... 7181 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (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 ... 7181 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssh-client_1%3a9.2p1-2+deb12u3_amd64.deb ... Unpacking openssh-client (1:9.2p1-2+deb12u3) over (1:9.2p1-2+deb12u2) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up openssh-client (1:9.2p1-2+deb12u3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-yf', 'dist-upgrade'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.6s DUMP: d8d332c94c6ed6182814c5286ffa0dd5 - 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m16.9s DUMP: Package: phyml Version: 3:3.3.20220408-3 Installed-Size: 4419 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libopenmpi3 (>= 4.1.4), 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_amd64.deb Size: 1103096 MD5sum: 05c8e5cf027e5f15ae1718f8fdd4670f SHA256: 219c33f8814f714589718d2ac2b00f002674d193a3700f2e7cec75e54f7549d1 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'show', '--no-all-versions', 'phyml'] 0m16.9s INFO: apt-cache knows about the following packages: phyml 0m16.9s INFO: Running scripts pre_install 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m17.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m17.1s DUMP: phyml: Installed: 3:3.3.20220408-3 Candidate: 3:3.3.20220408-3 Version table: *** 3:3.3.20220408-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml'] 0m17.7s DUMP: Reading package lists... Building dependency tree... Reading state information... phyml is already the newest version (3:3.3.20220408-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml'] 0m17.7s INFO: Running scripts post_install 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m17.7s INFO: Running scripts post_distupgrade 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m18.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m18.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m18.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m18.5s INFO: Running scripts pre_install 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_database-server'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_exceptions'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_extras'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m18.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m18.6s DUMP: phyml: Installed: 3:3.3.20220408-3 Candidate: 3:3.3.20220408-3 Version table: *** 3:3.3.20220408-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-cache', 'policy', 'phyml'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml=3:3.3.20220408-3'] 0m19.2s DUMP: Reading package lists... Building dependency tree... Reading state information... phyml is already the newest version (3:3.3.20220408-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', '-y', 'install', 'phyml=3:3.3.20220408-3'] 0m19.2s INFO: Running scripts post_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_install_exceptions'] 0m19.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m19.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m19.7s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m19.8s INFO: /bin converted to /usr/bin by /usr merge 0m19.8s INFO: /lib converted to /usr/lib by /usr merge 0m19.8s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m19.8s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m19.8s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m19.8s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m19.8s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m19.8s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m19.8s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m19.8s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m19.8s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m19.8s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m19.8s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m19.8s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m19.8s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m19.8s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m19.8s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m19.8s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m19.8s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m19.8s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m19.8s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m19.8s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m19.8s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m19.8s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m19.8s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m19.8s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m19.8s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m19.8s INFO: /sbin converted to /usr/sbin by /usr merge 0m20.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', '-ac', '--ignore-obsolete'] 0m21.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s DUMP: 0.15.6 0m21.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.0s INFO: Running adequate version 0.15.6 now. 0m21.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'phyml'] 0m21.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'phyml'] 0m21.1s INFO: Running scripts pre_remove 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.8s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed ibverbs-providers:amd64 ibverbs-providers 44.0-2 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcbor0.8:amd64 libcbor0.8 0.8.0-2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libedit2:amd64 libedit2 3.1-20221030-2 install ok installed libevent-core-2.1-7:amd64 libevent-core-2.1-7 2.1.12-stable-8 install ok installed libevent-pthreads-2.1-7:amd64 libevent-pthreads-2.1-7 2.1.12-stable-8 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libfabric1:amd64 libfabric1 1.17.0-3 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfido2-1:amd64 libfido2-1 1.12.0-2+b1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.9.0-1 install ok installed libhwloc15:amd64 libhwloc15 2.9.0-1 install ok installed libibverbs1:amd64 libibverbs1 44.0-2 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libmunge2 libmunge2 0.5.15-2 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.2+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.2+b1 install ok installed libnuma1:amd64 libnuma1 2.0.16-1 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.4-3+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpmix2:amd64 libpmix2 4.2.2-1+deb12u1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.2 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed librdmacm1:amd64 librdmacm1 44.0-2 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libucx0:amd64 libucx0 1.13.1-1 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 install ok installed libxnvctrl0:amd64 libxnvctrl0 525.85.05-3~deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.1-1 install ok installed openmpi-bin openmpi-bin 4.1.4-3+b1 install ok installed openmpi-common openmpi-common 4.1.4-3 install ok installed openssh-client openssh-client 1:9.2p1-2+deb12u3 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed phyml phyml 3:3.3.20220408-3 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'remove', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'phyml'] 0m25.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ibverbs-providers libatomic1 libbsd0 libcbor0.8 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client phyml 0 upgraded, 0 newly installed, 43 to remove and 0 not upgraded. After this operation, 84.5 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 ... 7181 files and directories currently installed.) Removing phyml (3:3.3.20220408-3) ... Removing openmpi-bin (4.1.4-3+b1) ... Removing libopenmpi3:amd64 (4.1.4-3+b1) ... Removing libucx0:amd64 (1.13.1-1) ... Removing libfabric1:amd64 (1.17.0-3) ... Removing ibverbs-providers:amd64 (44.0-2) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing libpmix2:amd64 (4.2.2-1+deb12u1) ... Removing libhwloc-plugins:amd64 (2.9.0-1) ... Removing libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing openssh-client (1:9.2p1-2+deb12u3) ... Removing libedit2:amd64 (3.1-20221030-2) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libfido2-1:amd64 (1.12.0-2+b1) ... Removing libcbor0.8:amd64 (0.8.0-2+b1) ... Removing libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Removing libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libhwloc15:amd64 (2.9.0-1) ... Removing librdmacm1:amd64 (44.0-2) ... Removing libibverbs1:amd64 (44.0-2) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libicu72:amd64 (72.1-3) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing libmunge2 (0.5.15-2) ... Removing libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.2+b1) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.16-1) ... Removing libpciaccess0:amd64 (0.17-2) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.1-1) ... Removing openmpi-common (4.1.4-3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'remove', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'phyml'] 0m25.0s INFO: Running scripts post_remove 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_remove_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_remove_exceptions'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client'] 0m25.2s DUMP: (Reading database ... 6120 files and directories currently installed.) Purging configuration files for ibverbs-providers:amd64 (44.0-2) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcbor0.8 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7 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 Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... 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 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 libmunge2 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.2+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 libopenmpi3 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpmix2 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.2) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1 which isn't installed dpkg: warning: ignoring request to remove libssl3 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 ocl-icd-libopencl1 which isn't installed Purging configuration files for openmpi-bin (4.1.4-3+b1) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.2p1-2+deb12u3) ... 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', 'phyml'] 0m25.2s DUMP: dpkg: warning: ignoring request to remove phyml which isn't installed 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', 'phyml'] 0m25.2s INFO: Running scripts post_purge 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_purge_exceptions'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_purge_exceptions'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', '--pending'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--purge', '--pending'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--remove', '--pending'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg', '--remove', '--pending'] 0m25.2s INFO: Running scripts post_test 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_test_exceptions'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'tmp/scripts/post_test_exceptions'] 0m25.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m25.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-divert', '--list'] 0m25.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'dpkg-divert', '--list'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'clean'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnwn920bb', 'apt-get', 'clean'] 0m25.7s DEBUG: Recording chroot state 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/shm'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/shm'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/console'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/console'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/ptmx'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/ptmx'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/dev/pts'] 0m26.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/proc'] 0m26.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnwn920bb/proc'] 0m26.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m26.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnwn920bb'] 0m26.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnwn920bb 0m26.8s INFO: PASS: Upgrading between Debian distributions. 0m26.8s INFO: PASS: All tests. 0m26.8s INFO: piuparts run ends. ret=0 End: 2024-08-21 18:28:45 GMT