Start: 2024-11-30 03:36:31 GMT [testing] Package: relion Source: relion (3.1.3-3) Version: 3.1.3-3+b2 Installed-Size: 96825 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3t64 (>= 4.1.6), libstdc++6 (>= 13.1), libtiff6 (>= 4.0.3) Conflicts: relion-cuda Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: a54d8123a50edf0f9102f8a3c05de97f Section: science Priority: optional Filename: pool/main/r/relion/relion_3.1.3-3+b2_amd64.deb Size: 15143952 MD5sum: bcaf09256084f5561823382aecab4f7e SHA256: cbd8725aaafe9ce1525080b05535d8842f983f5c03aeafb01c1a3dc9ffd8c7e5 [sid] Package: relion Source: relion (3.1.3-4) Version: 3.1.3-4+b1 Installed-Size: 101385 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Depends: mpi-default-bin, libc6 (>= 2.38), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 14), libtiff6 (>= 4.0.3) Conflicts: relion-cuda Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: a54d8123a50edf0f9102f8a3c05de97f Section: science Priority: optional Filename: pool/main/r/relion/relion_3.1.3-4+b1_amd64.deb Size: 15640312 MD5sum: d677e86c68921e13cf003c1973565d74 SHA256: b45ca37a9aa6cf4f0eff18caa25c5fbe69d73078cf7b0eb887cc7969f332a153 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 relion=3.1.3-4+b1 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 relion=3.1.3-4+b1 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/tmpywh8qk7o 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpywh8qk7o 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '--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/tmpywh8qk7o', '--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/tmpywh8qk7o/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/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/tmpywh8qk7o/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/tmpywh8qk7o/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/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/tmpywh8qk7o/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'update'] 0m1.7s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9376 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6274 kB] Fetched 15.8 MB in 1s (16.0 MB/s) Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libcap-ng0 libseccomp2 libsystemd0 libudev1 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 660 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257~rc3-1 [448 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257~rc3-1 [147 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 660 kB in 0s (8032 kB/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 ... 5150 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-4_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4) over (0.8.5-3+b1) ... Setting up libcap-ng0:amd64 (0.8.5-4) ... (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 ... 5149 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libsystemd0_257~rc3-1_amd64.deb ... Unpacking libsystemd0:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libsystemd0:amd64 (257~rc3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5148 files and directories currently installed.) Preparing to unpack .../libudev1_257~rc3-1_amd64.deb ... Unpacking libudev1:amd64 (257~rc3-1) over (257~rc2-3) ... Setting up libudev1:amd64 (257~rc3-1) ... Processing triggers for libc-bin (2.40-3) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: a428c05501a6d82400f5caecb5f9d890 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '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/tmpywh8qk7o', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '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/tmpywh8qk7o', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '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/tmpywh8qk7o', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 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 1:2.40.2-11 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 5.21 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 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 0.8.5-4 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 0.273 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 3.8.8-2 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 2.40.2-11 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 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 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~rc3-1 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 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 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+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 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 2.40.2-11 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 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 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 2.40.2-11 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/tmpywh8qk7o', '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 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m3.1s INFO: Running scripts is_testable 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s INFO: Running scripts pre_test 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '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/tmpywh8qk7o', 'tmp/scripts/pre_test_root_password'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'show', '--no-all-versions', 'relion'] 0m3.3s DUMP: Package: relion Source: relion (3.1.3-3) Version: 3.1.3-3+b2 Installed-Size: 96825 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Depends: openmpi-gcc | openmpi-bin, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3t64 (>= 4.1.6), libstdc++6 (>= 13.1), libtiff6 (>= 4.0.3) Conflicts: relion-cuda Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description-en: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support. . relion provides the serial and parallel (MPI) command-line tools without CUDA/GPU support. Description-md5: a54d8123a50edf0f9102f8a3c05de97f Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Section: science Priority: optional Filename: pool/main/r/relion/relion_3.1.3-3+b2_amd64.deb Size: 15143952 MD5sum: bcaf09256084f5561823382aecab4f7e SHA256: cbd8725aaafe9ce1525080b05535d8842f983f5c03aeafb01c1a3dc9ffd8c7e5 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'show', '--no-all-versions', 'relion'] 0m3.3s INFO: apt-cache knows about the following packages: relion 0m3.3s INFO: Running scripts pre_install 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m3.3s 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: 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m3.3s DUMP: relion: Installed: (none) Candidate: 3.1.3-3+b2 Version table: 3.1.3-3+b2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion'] 0m9.3s 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 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 libwebp7 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 libfftw3-bin libfftw3-dev 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 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 libwebp7 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 relion 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 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libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 relion amd64 3.1.3-3+b2 [15.1 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 2s (44.3 MB/s) Selecting previously unselected package adduser. 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Setting up libdeflate0:amd64 (1.22-1) ... Setting up libibmad5:amd64 (52.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... 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 libfftw3-double3:amd64 (3.3.10-1+b3) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... 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 (2:1.8.10-2) ... 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+really2.9.14-0.2+b1) ... Setting up libfftw3-single3:amd64 (3.3.10-1+b3) ... 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 (5.40.0-8) ... Setting up perl (5.40.0-8) ... 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 (5.0.4-1) ... 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 relion (3.1.3-3+b2) ... Processing triggers for libc-bin (2.40-3) ... 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion'] 0m9.3s INFO: Running scripts post_install 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m9.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m9.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m9.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpywh8qk7o to sid 0m9.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.6s INFO: Running scripts pre_distupgrade 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'update'] 0m11.9s 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 [7339 kB] Fetched 17.6 MB in 2s (9940 kB/s) Reading package lists... 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'update'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-yf', 'dist-upgrade'] 0m15.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libopenmpi3t64 The following NEW packages will be installed: libopenmpi40 mpi-default-bin The following packages will be upgraded: apt e2fsprogs libapt-pkg6.0t64 libc-bin libc6 libcom-err2 libdebconfclient0 libext2fs2t64 libfftw3-double3 libfftw3-single3 libhsa-runtime64-1 libhsakmt1 libss2 logsave openmpi-bin openmpi-common relion 17 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. Need to get 27.3 MB of archives. After this operation, 5771 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.16 [1113 kB] Get:3 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.16 [1397 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Get:5 http://deb.debian.org/debian sid/main amd64 relion amd64 3.1.3-4+b1 [15.6 MB] Get:6 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 5.0.6-2 [189 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libopenmpi40 amd64 5.0.6-2 [2366 kB] Get:8 http://deb.debian.org/debian sid/main amd64 openmpi-common all 5.0.6-2 [97.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get:10 http://deb.debian.org/debian sid/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get:12 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.2~rc1-1 [23.5 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.2~rc1-1 [211 kB] Get:14 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.2~rc1-1 [589 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.274 [10.1 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2~rc1-1 [23.6 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 libss2 amd64 1.47.2~rc1-1 [28.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.3 MB in 2s (17.3 MB/s) (Reading database ... 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(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 ... 8663 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-4_amd64.deb ... Unpacking libc-bin (2.40-4) over (2.40-3) ... Setting up libc-bin (2.40-4) ... (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 ... 8663 files and directories currently installed.) Preparing to unpack .../relion_3.1.3-4+b1_amd64.deb ... Unpacking relion (3.1.3-4+b1) over (3.1.3-3+b2) ... Preparing to unpack .../openmpi-bin_5.0.6-2_amd64.deb ... Unpacking openmpi-bin (5.0.6-2) over (4.1.6-13.3) ... (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 ... 8637 files and directories currently installed.) Removing libopenmpi3t64:amd64 (4.1.6-13.3) ... Selecting previously unselected package libopenmpi40: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 ... 8468 files and directories currently installed.) Preparing to unpack .../0-libopenmpi40_5.0.6-2_amd64.deb ... Unpacking libopenmpi40:amd64 (5.0.6-2) ... Preparing to unpack .../1-openmpi-common_5.0.6-2_all.deb ... Unpacking openmpi-common (5.0.6-2) over (4.1.6-13.3) ... Selecting previously unselected package mpi-default-bin. Preparing to unpack .../2-mpi-default-bin_1.17_amd64.deb ... Unpacking mpi-default-bin (1.17) ... Preparing to unpack .../3-libfftw3-double3_3.3.10-2+b1_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2+b1) over (3.3.10-1+b3) ... Preparing to unpack .../4-libfftw3-single3_3.3.10-2+b1_amd64.deb ... Unpacking libfftw3-single3:amd64 (3.3.10-2+b1) over (3.3.10-1+b3) ... Preparing to unpack .../5-logsave_1.47.2~rc1-1_amd64.deb ... Unpacking logsave (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../6-libext2fs2t64_1.47.2~rc1-1_amd64.deb ... Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving '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' Unpacking libext2fs2t64:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Setting up libext2fs2t64:amd64 (1.47.2~rc1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8558 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.2~rc1-1_amd64.deb ... Unpacking e2fsprogs (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../libdebconfclient0_0.274_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.274) over (0.273) ... Setting up libdebconfclient0:amd64 (0.274) ... (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 ... 8557 files and directories currently installed.) Preparing to unpack .../libcom-err2_1.47.2~rc1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Preparing to unpack .../libhsakmt1_6.1.2+ds-1_amd64.deb ... Unpacking libhsakmt1:amd64 (6.1.2+ds-1) over (5.7.0-1) ... Preparing to unpack .../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 .../libss2_1.47.2~rc1-1_amd64.deb ... Unpacking libss2:amd64 (1.47.2~rc1-1) over (1.47.1-1+b1) ... Setting up libopenmpi40:amd64 (5.0.6-2) ... Setting up libfftw3-single3:amd64 (3.3.10-2+b1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-1) ... Setting up libss2:amd64 (1.47.2~rc1-1) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up logsave (1.47.2~rc1-1) ... Setting up openmpi-common (5.0.6-2) ... Setting up openmpi-bin (5.0.6-2) ... 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 Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up mpi-default-bin (1.17) ... Setting up relion (3.1.3-4+b1) ... Setting up e2fsprogs (1.47.2~rc1-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Processing triggers for libc-bin (2.40-4) ... 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-yf', 'dist-upgrade'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.1s DUMP: 7e12fa197c1ebec89a367e5a26d7f5af - 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'show', '--no-all-versions', 'relion'] 0m16.2s DUMP: Package: relion Source: relion (3.1.3-4) Version: 3.1.3-4+b1 Installed-Size: 101385 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Depends: mpi-default-bin, libc6 (>= 2.38), libfftw3-double3 (>= 3.3.10), libfftw3-single3 (>= 3.3.10), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi40 (>= 5.0.6), libstdc++6 (>= 14), libtiff6 (>= 4.0.3) Conflicts: relion-cuda Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description-en: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions, optionally with CUDA/GPU support. . relion provides the serial and parallel (MPI) command-line tools without CUDA/GPU support. Description-md5: a54d8123a50edf0f9102f8a3c05de97f Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Section: science Priority: optional Filename: pool/main/r/relion/relion_3.1.3-4+b1_amd64.deb Size: 15640312 MD5sum: d677e86c68921e13cf003c1973565d74 SHA256: b45ca37a9aa6cf4f0eff18caa25c5fbe69d73078cf7b0eb887cc7969f332a153 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'show', '--no-all-versions', 'relion'] 0m16.2s INFO: apt-cache knows about the following packages: relion 0m16.2s INFO: Running scripts pre_install 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m16.3s 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: 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m16.3s DUMP: relion: Installed: 3.1.3-4+b1 Candidate: 3.1.3-4+b1 Version table: *** 3.1.3-4+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion'] 0m16.5s DUMP: Reading package lists... Building dependency tree... Reading state information... relion is already the newest version (3.1.3-4+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion'] 0m16.5s INFO: Running scripts post_install 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m16.5s INFO: Running scripts post_distupgrade 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m16.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m16.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m17.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m17.1s INFO: Running scripts pre_install 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_database-server'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_exceptions'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_extras'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m17.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m17.2s DUMP: relion: Installed: 3.1.3-4+b1 Candidate: 3.1.3-4+b1 Version table: *** 3.1.3-4+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-cache', 'policy', 'relion'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion=3.1.3-4+b1'] 0m17.5s DUMP: Reading package lists... Building dependency tree... Reading state information... relion is already the newest version (3.1.3-4+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', '-y', 'install', 'relion=3.1.3-4+b1'] 0m17.5s INFO: Running scripts post_install 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_install_exceptions'] 0m17.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m17.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m18.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '-ac', '--ignore-obsolete'] 0m19.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', '-ac', '--ignore-obsolete'] 0m19.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.2s DUMP: 0.15.6 0m19.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.2s INFO: Running adequate version 0.15.6 now. 0m19.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'relion'] 0m19.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'relion'] 0m19.7s INFO: Running scripts pre_remove 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.6s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/pre_remove_exceptions'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.7s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 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 1:2.40.2-11 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 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-1 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 2.9.16 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 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 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 1.47.2~rc1-1 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 0.274 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 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 1.47.2~rc1-1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3.1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.10-2+b1 install ok installed libfftw3-single3:amd64 libfftw3-single3 3.3.10-2+b1 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 3.8.8-2 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 libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+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 liblerc4:amd64 liblerc4 4.0.0+ds-5 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 2.40.2-11 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 libopenmpi40:amd64 libopenmpi40 5.0.6-2 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 10.44-4 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.4-1 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 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.2~rc1-1 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~rc3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 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~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 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 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 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+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.2~rc1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 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 5.0.6-2 install ok installed openmpi-common openmpi-common 5.0.6-2 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 1:4.16.0-5 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed relion relion 3.1.3-4+b1 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 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdeflate0: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', 'libfftw3-double3:amd64', 'libfftw3-single3: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', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libsharpyuv0:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7: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', 'relion'] 0m21.3s 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 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libgdbm-compat4t64 libgdbm6t64 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libllvm17t64 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40 libpciaccess0 libperl5.40 libpmix2t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 libwebp7 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 relion 0 upgraded, 0 newly installed, 70 to remove and 0 not upgraded. After this operation, 485 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 ... 8555 files and directories currently installed.) Removing relion (3.1.3-4+b1) ... Removing mpi-default-bin (1.17) ... Removing openmpi-bin (5.0.6-2) ... Removing libopenmpi40:amd64 (5.0.6-2) ... 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 libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... 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 (5.0.4-1) ... 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 libfftw3-double3:amd64 (3.3.10-2+b1) ... Removing libfftw3-single3:amd64 (3.3.10-2+b1) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... 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+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+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 liblerc4:amd64 (4.0.0+ds-5) ... 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 libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... 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 (1:1.1.5-1) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Removing openmpi-common (5.0.6-2) ... Removing perl-modules-5.40 (5.40.0-8) ... 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 (2.40-4) ... 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdeflate0: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', 'libfftw3-double3:amd64', 'libfftw3-single3: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', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libsharpyuv0:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7: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', 'relion'] 0m21.3s INFO: Running scripts post_remove 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_remove_exceptions'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_remove_exceptions'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdeflate0: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', 'libfftw3-double3:amd64', 'libfftw3-single3: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', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libsharpyuv0:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7: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'] 0m21.4s DUMP: (Reading database ... 5182 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 libdeflate0 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 libfftw3-double3 which isn't installed dpkg: warning: ignoring request to remove libfftw3-single3 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 libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo 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 liblerc4 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 libopenmpi40 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 libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libwebp7 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 (5.0.6-2) ... 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 (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libcbor0.10:amd64', 'libdeflate0: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', 'libfftw3-double3:amd64', 'libfftw3-single3: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', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libpciaccess0:amd64', 'libperl5.40:amd64', 'libpmix2t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'libsharpyuv0:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7: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'] 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', 'relion'] 0m21.4s DUMP: dpkg: warning: ignoring request to remove relion which isn't installed 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', 'relion'] 0m21.4s INFO: Running scripts post_purge 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_purge_exceptions'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_purge_exceptions'] 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', '--pending'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--purge', '--pending'] 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--remove', '--pending'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg', '--remove', '--pending'] 0m21.4s INFO: Running scripts post_test 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_test_exceptions'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'tmp/scripts/post_test_exceptions'] 0m21.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m21.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg-divert', '--list'] 0m21.6s 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 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'dpkg-divert', '--list'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'clean'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o', 'apt-get', 'clean'] 0m21.6s DEBUG: Recording chroot state 0m21.9s 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 0m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/shm'] 0m22.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/shm'] 0m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/console'] 0m22.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/console'] 0m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/ptmx'] 0m22.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/ptmx'] 0m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/pts'] 0m22.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/dev/pts'] 0m22.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/proc'] 0m22.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o/proc'] 0m22.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m22.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpywh8qk7o'] 0m22.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpywh8qk7o 0m22.2s INFO: PASS: Upgrading between Debian distributions. 0m22.2s INFO: PASS: All tests. 0m22.2s INFO: piuparts run ends. ret=0 End: 2024-11-30 03:36:53 GMT