Start: 2024-11-06 05:45:59 GMT Package: relion-gui Source: relion (3.1.3-3) Version: 3.1.3-3+b1 Installed-Size: 5337 Maintainer: Debian Med Packaging Team Architecture: amd64 Replaces: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Depends: relion (= 3.1.3-3+b1), libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libfltk1.3 (>= 1.3.4), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11), libtiff6 (>= 4.0.3) Conflicts: relion-cuda-gui Breaks: relion-bin, relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps) Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: 17b4d8288a7b95c56b60109e77e4b7c3 Section: science Priority: optional Filename: pool/main/r/relion/relion-gui_3.1.3-3+b1_amd64.deb Size: 1158200 MD5sum: 024ca5d5694ed25b1ddf5a6e1b2a1e1b SHA256: 40d52bb260371989e6c5714f4cacc20c7570131c746850a6f1beeb290d4bcf65 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-log-alternatives --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 --no-upgrade-test --apt relion-gui=3.1.3-3+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-log-alternatives --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 --no-upgrade-test --apt relion-gui=3.1.3-3+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/tmpw4v73her 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpw4v73her 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpw4v73her', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpw4v73her', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpw4v73her/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpw4v73her/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/tmpw4v73her/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/tmpw4v73her/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm 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-log-alternatives to /srv/piuparts.debian.org/tmp/tmpw4v73her/tmp/scripts/ 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpw4v73her/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'update'] 0m0.7s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'update'] 0m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s DUMP: 14b5c1b94e8a6c425b0bba0e4df4ee12 - 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s INFO: Running scripts post_setup 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'clean'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'clean'] 0m1.6s DEBUG: Recording chroot state 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.8s 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+deb12u7 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+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 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 252.30-1~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 252.30-1~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 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-divert', '--list'] 0m1.8s 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 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-divert', '--list'] 0m1.8s INFO: Running scripts is_testable 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s INFO: apt-cache does not know about any of the requested packages 0m1.8s INFO: Running scripts pre_test 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_test_root_password'] 0m1.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_test_root_password'] 0m1.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m2.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m2.3s DEBUG: No broken symlinks as far as we can find. 0m2.3s INFO: Running scripts pre_install 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_database-server'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_database-server'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_exceptions'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_exceptions'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_extras'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_extras'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_log_alternatives'] 0m2.4s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_install_log_alternatives'] 0m2.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m2.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m2.9s DEBUG: No broken symlinks as far as we can find. 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-cache', 'policy'] 0m3.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.7,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-cache', 'policy'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-cache', 'policy', 'relion-gui'] 0m3.3s DUMP: relion-gui: Installed: (none) Candidate: 3.1.3-3+b1 Version table: 3.1.3-3+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-cache', 'policy', 'relion-gui'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', '-y', 'install', 'relion-gui=3.1.3-3+b1'] 0m7.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fontconfig-config fonts-dejavu-core ibverbs-providers libatomic1 libbrotli1 libbsd0 libcbor0.8 libdeflate0 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libfltk1.3 libfontconfig1 libfreetype6 libgomp1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpng16-16 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libtiff6 libucx0 libwebp7 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client relion Suggested packages: libfftw3-bin libfftw3-dev 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: fontconfig-config fonts-dejavu-core ibverbs-providers libatomic1 libbrotli1 libbsd0 libcbor0.8 libdeflate0 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libfltk1.3 libfontconfig1 libfreetype6 libgomp1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpng16-16 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libtiff6 libucx0 libwebp7 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client relion relion-gui 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 44.3 MB of archives. After this operation, 201 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 3.0.14-1~deb12u1 [2024 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+deb12u2 [32.6 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 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+deb12u2 [332 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2+deb12u3 [991 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:19 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libfftw3-double3 amd64 3.3.10-1 [776 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libfftw3-single3 amd64 3.3.10-1 [806 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libfltk1.3 amd64 1.3.8-5 [569 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-3~deb12u1 [13.5 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+deb12u1 [622 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 relion amd64 3.1.3-3+b1 [15.1 MB] Get:66 http://deb.debian.org/debian bookworm/main amd64 relion-gui amd64 3.1.3-3+b1 [1158 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.3 MB in 1s (42.2 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 ... 6094 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_3.0.14-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.14-1~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+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) ... 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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Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../43-libxft2_2.3.6-1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1) ... Selecting previously unselected package libxinerama1:amd64. Preparing to unpack .../44-libxinerama1_2%3a1.1.4-3_amd64.deb ... Unpacking libxinerama1:amd64 (2:1.1.4-3) ... Selecting previously unselected package libfltk1.3:amd64. Preparing to unpack .../45-libfltk1.3_1.3.8-5_amd64.deb ... Unpacking libfltk1.3:amd64 (1.3.8-5) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../46-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../47-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../48-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../49-libxnvctrl0_525.85.05-3~deb12u1_amd64.deb ... Unpacking libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../50-ocl-icd-libopencl1_2.3.1-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../51-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../52-libhwloc-plugins_2.9.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.9.0-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../53-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../54-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../55-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libmunge2. Preparing to unpack .../56-libmunge2_0.5.15-2_amd64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../57-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 .../58-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../59-libopenmpi3_4.1.4-3+b1_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.4-3+b1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../60-libwebp7_1.2.4-0.2+deb12u1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../61-libtiff6_4.5.0-6+deb12u1_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-6+deb12u1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../62-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../63-openmpi-bin_4.1.4-3+b1_amd64.deb ... Unpacking openmpi-bin (4.1.4-3+b1) ... Selecting previously unselected package relion. Preparing to unpack .../64-relion_3.1.3-3+b1_amd64.deb ... Unpacking relion (3.1.3-3+b1) ... Selecting previously unselected package relion-gui. Preparing to unpack .../65-relion-gui_3.1.3-3+b1_amd64.deb ... Unpacking relion-gui (3.1.3-3+b1) ... Setting up libexpat1:amd64 (2.5.0-1) ... 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 liblerc4:amd64 (4.0.0+ds-2) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.14-1~deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libmunge2 (0.5.15-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libpng16-16:amd64 (1.6.39-2) ... 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 fonts-dejavu-core (2.37-6) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up libfftw3-double3:amd64 (3.3.10-1) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... 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+deb12u2) ... 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 libfftw3-single3:amd64 (3.3.10-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2+deb12u3) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... 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 libfltk1.3:amd64 (1.3.8-5) ... 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 relion (3.1.3-3+b1) ... Setting up relion-gui (3.1.3-3+b1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', '-y', 'install', 'relion-gui=3.1.3-3+b1'] 0m7.2s INFO: Running scripts post_install 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_install_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_install_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_install_log_alternatives'] 0m7.2s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=libpsm-infinipath1: piuparts=relion-gui=3.1.3-3+b1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 libpsm_infinipath.so.1 /usr/lib/libpsm1/libpsm_infinipath.so.1.16 40 LOG-ALTERNATIVES: dpkg=openmpi-bin: piuparts=relion-gui=3.1.3-3+b1: /usr/bin/update-alternatives --install /usr/bin/mpirun mpirun /usr/bin/mpirun.openmpi 50 --slave /usr/share/man/man1/mpirun.1.gz mpirun.1.gz /usr/share/man/man1/mpirun.openmpi.1.gz --slave /usr/bin/mpiexec mpiexec /usr/bin/mpiexec.openmpi --slave /usr/share/man/man1/mpiexec.1.gz mpiexec.1.gz /usr/share/man/man1/mpiexec.openmpi.1.gz LOG-ALTERNATIVES: dpkg=openmpi-bin: piuparts=relion-gui=3.1.3-3+b1: /usr/bin/update-alternatives --install /usr/bin/mpicc mpi /usr/bin/mpicc.openmpi 50 --slave /usr/bin/mpic++ mpic++ /usr/bin/mpic++.openmpi --slave /usr/bin/mpicxx mpicxx /usr/bin/mpic++.openmpi --slave /usr/bin/mpiCC mpiCC /usr/bin/mpic++.openmpi --slave /usr/bin/mpif77 mpif77 /usr/bin/mpif77.openmpi --slave /usr/bin/mpif90 mpif90 /usr/bin/mpif90.openmpi --slave /usr/bin/mpifort mpifort /usr/bin/mpifort.openmpi --slave /usr/share/man/man1/mpicc.1.gz mpicc.1.gz /usr/share/man/man1/mpicc.openmpi.1.gz --slave /usr/share/man/man1/mpic++.1.gz mpic++.1.gz /usr/share/man/man1/mpic++.openmpi.1.gz --slave /usr/share/man/man1/mpicxx.1.gz mpicxx.1.gz /usr/share/man/man1/mpicxx.openmpi.1.gz --slave /usr/share/man/man1/mpiCC.1.gz mpiCC.1.gz /usr/share/man/man1/mpiCC.openmpi.1.gz --slave /usr/share/man/man1/mpif77.1.gz mpif77.1.gz /usr/share/man/man1/mpif77.openmpi.1.gz --slave /usr/share/man/man1/mpif90.1.gz mpif90.1.gz /usr/share/man/man1/mpif90.openmpi.1.gz --slave /usr/share/man/man1/mpifort.1.gz mpifort.1.gz /usr/share/man/man1/mpifort.openmpi.1.gz 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_install_log_alternatives'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m7.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m7.9s ERROR: WARN: Broken symlinks: /usr/share/doc/libucx0/README -> README.md (libucx0:amd64) 0m7.9s INFO: /bin converted to /usr/bin by /usr merge 0m7.9s INFO: /lib converted to /usr/lib by /usr merge 0m7.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m7.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m7.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m7.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m7.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m7.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m7.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m7.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m7.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m7.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m7.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m7.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m7.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m7.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m7.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m7.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m7.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m7.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m7.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m7.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m7.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m7.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m7.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m7.9s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m7.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m7.9s INFO: /sbin converted to /usr/sbin by /usr merge 0m8.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpw4v73her', '-ac', '--ignore-obsolete'] 0m8.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpw4v73her', '-ac', '--ignore-obsolete'] 0m8.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.8s DUMP: 0.15.6 0m8.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.8s INFO: Running adequate version 0.15.6 now. 0m8.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'relion-gui'] 0m8.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'relion-gui'] 0m8.9s INFO: Running scripts pre_remove 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_exceptions'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/pre_remove_exceptions'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.1s 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+deb12u7 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 fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 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 libbrotli1:amd64 libbrotli1 1.0.9-2+b6 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 libdeflate0:amd64 libdeflate0 1.14-1 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 libexpat1:amd64 libexpat1 2.5.0-1 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 libfftw3-double3:amd64 libfftw3-double3 3.3.10-1 install ok installed libfftw3-single3:amd64 libfftw3-single3 3.3.10-1 install ok installed libfido2-1:amd64 libfido2-1 1.12.0-2+b1 install ok installed libfltk1.3:amd64 libfltk1.3 1.3.8-5 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 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 libgomp1:amd64 libgomp1 12.2.0-14 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 libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 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 liblerc4:amd64 liblerc4 4.0.0+ds-2 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 libpng16-16:amd64 libpng16-16 1.6.39-2 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 3.0.14-1~deb12u1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.30-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 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 252.30-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+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 libxcursor1:amd64 libxcursor1 1:1.2.1-1 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 libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 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 libxrender1:amd64 libxrender1 1:0.9.10-1.1 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 relion relion 3.1.3-3+b1 install ok installed relion-gui relion-gui 3.1.3-3+b1 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 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libdeflate0:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfido2-1:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'relion', 'relion-gui'] 0m10.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fontconfig-config fonts-dejavu-core ibverbs-providers libatomic1 libbrotli1 libbsd0 libcbor0.8 libdeflate0 libedit2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-double3 libfftw3-single3 libfido2-1 libfltk1.3 libfontconfig1 libfreetype6 libgomp1 libgssapi-krb5-2 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblerc4 libmunge2 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libpng16-16 libpsm-infinipath1 libpsm2-2 librdmacm1 libssl3 libtiff6 libucx0 libwebp7 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxnvctrl0 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client relion relion-gui 0 upgraded, 0 newly installed, 66 to remove and 0 not upgraded. After this operation, 201 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 ... 7489 files and directories currently installed.) Removing relion-gui (3.1.3-3+b1) ... Removing libfltk1.3:amd64 (1.3.8-5) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing relion (3.1.3-3+b1) ... 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 libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... 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 openssh-client (1:9.2p1-2+deb12u3) ... Removing libedit2:amd64 (3.1-20221030-2) ... Removing libfido2-1:amd64 (1.12.0-2+b1) ... Removing libcbor0.8:amd64 (0.8.0-2+b1) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... 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 libexpat1:amd64 (2.5.0-1) ... Removing libfftw3-double3:amd64 (3.3.10-1) ... Removing libfftw3-single3:amd64 (3.3.10-1) ... Removing libgomp1:amd64 (12.2.0-14) ... 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 libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... 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 liblerc4:amd64 (4.0.0+ds-2) ... 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 libpng16-16:amd64 (1.6.39-2) ... 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 (3.0.14-1~deb12u1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing ocl-icd-libopencl1:amd64 (2.3.1-1) ... Removing openmpi-common (4.1.4-3) ... 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 libbsd0:amd64 (0.11.7-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libdeflate0:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfido2-1:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'relion', 'relion-gui'] 0m10.9s INFO: Running scripts post_remove 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_remove_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_remove_exceptions'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libdeflate0:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfido2-1:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'relion'] 0m11.2s DUMP: (Reading database ... 6137 files and directories currently installed.) Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... 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 libbrotli1 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 libdeflate0 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 libexpat1 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 libfltk1.3 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgomp1 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 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 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 dpkg: warning: ignoring request to remove libpng16-16 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 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 libxcursor1 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 libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 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 libxrender1 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) ... dpkg: warning: ignoring request to remove relion which isn't installed 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.8:amd64', 'libdeflate0:amd64', 'libedit2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libexpat1:amd64', 'libfabric1:amd64', 'libfftw3-double3:amd64', 'libfftw3-single3:amd64', 'libfido2-1:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblerc4:amd64', 'libmunge2', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libucx0:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'relion'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', 'relion-gui'] 0m11.3s DUMP: dpkg: warning: ignoring request to remove relion-gui which isn't installed 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', 'relion-gui'] 0m11.3s INFO: Running scripts post_purge 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_purge_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_purge_exceptions'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', '--pending'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--purge', '--pending'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--remove', '--pending'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg', '--remove', '--pending'] 0m11.3s INFO: Running scripts post_test 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_test_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'tmp/scripts/post_test_exceptions'] 0m11.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m11.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m11.8s DEBUG: No broken symlinks as far as we can find. 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-divert', '--list'] 0m11.8s 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 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'dpkg-divert', '--list'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'clean'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpw4v73her', 'apt-get', 'clean'] 0m11.8s DEBUG: Recording chroot state 0m12.1s INFO: PASS: Installation and purging test. 0m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/shm'] 0m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/shm'] 0m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/console'] 0m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/console'] 0m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/ptmx'] 0m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/ptmx'] 0m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/pts'] 0m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/dev/pts'] 0m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/proc'] 0m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpw4v73her/proc'] 0m12.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m12.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpw4v73her'] 0m12.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpw4v73her 0m12.5s INFO: PASS: All tests. 0m12.5s INFO: piuparts run ends. ret=0 End: 2024-11-06 05:46:11 GMT