Start: 2023-03-25 23:49:38 GMT Package: relion-bin+mpi+gui Source: relion (1.4+dfsg-2) Version: 1.4+dfsg-2+b2 Installed-Size: 1406 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libfftw3-double3 (>= 3.3.5), libfltk1.3, libgcc1 (>= 1:3.0), libopenmpi2, librelion+mpi+gui-1.4-1, libstdc++6 (>= 5.2), libx11-6, openmpi-gcc | openmpi-bin Conflicts: relion-bin, relion-bin+gui, relion-bin+mpi Description: parallel toolkit for 3D reconstructions in cryo-electron microscopy Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: c45f291e5e68464ccf6fbf15740cef16 Section: science Priority: optional Filename: pool/main/r/relion/relion-bin+mpi+gui_1.4+dfsg-2+b2_amd64.deb Size: 244926 MD5sum: 64feed86e6abbe3f01e2c1ab2346097b SHA256: bbc45ae7bfa8fb54ffe52876703b67dba8329c240cf5c040ac4a5234dca00546 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt relion-bin+mpi+gui=1.4+dfsg-2+b2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt relion-bin+mpi+gui=1.4+dfsg-2+b2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpx3r5tin7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpx3r5tin7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Created resolv.conf. 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpx3r5tin7/tmp/scripts/ 0m1.4s INFO: Running scripts post_chroot_unpack 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'update'] 0m2.1s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'clean'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'clean'] 0m3.7s DEBUG: Recording chroot state 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-divert', '--list'] 0m4.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-divert', '--list'] 0m4.0s INFO: Running scripts is_testable 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/is_testable_uninstallable'] 0m4.0s INFO: apt-cache does not know about any of the requested packages 0m4.0s INFO: Running scripts pre_test 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_test_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_test_root_password'] 0m4.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_test_root_password'] 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m4.6s DEBUG: No broken symlinks as far as we can find. 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m5.1s DEBUG: No broken symlinks as far as we can find. 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-cache', 'policy'] 0m5.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-cache', 'policy'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-cache', 'policy', 'relion-bin+mpi+gui'] 0m5.7s DUMP: relion-bin+mpi+gui: Installed: (none) Candidate: 1.4+dfsg-2+b2 Version table: 1.4+dfsg-2+b2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-cache', 'policy', 'relion-bin+mpi+gui'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', '-y', 'install', 'relion-bin+mpi+gui=1.4+dfsg-2+b2'] 0m10.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fontconfig-config fonts-dejavu-core libbsd0 libexpat1 libfabric1 libfftw3-double3 libfltk1.3 libfontconfig1 libfreetype6 libgfortran3 libgomp1 libhwloc-plugins libhwloc5 libibverbs1 libicu57 libltdl7 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi2 libpciaccess0 libpng16-16 libpsm-infinipath1 libquadmath0 librdmacm1 librelion+mpi+gui-1.4-1 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common sgml-base ucf xml-core Suggested packages: libfftw3-bin libfftw3-dev libhwloc-contrib-plugins pciutils opencl-icd gfortran sgml-base-doc debhelper The following NEW packages will be installed: fontconfig-config fonts-dejavu-core libbsd0 libexpat1 libfabric1 libfftw3-double3 libfltk1.3 libfontconfig1 libfreetype6 libgfortran3 libgomp1 libhwloc-plugins libhwloc5 libibverbs1 libicu57 libltdl7 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi2 libpciaccess0 libpng16-16 libpsm-infinipath1 libquadmath0 librdmacm1 librelion+mpi+gui-1.4-1 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common relion-bin+mpi+gui sgml-base ucf xml-core 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 19.1 MB of archives. After this operation, 64.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 sgml-base all 1.29 [14.8 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2+deb9u2 [920 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 ucf all 3.0036 [70.2 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libibverbs1 amd64 1.2.1-2 [39.3 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [169 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 librdmacm1 amd64 1.1.0-2 [49.4 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libfabric1 amd64 1.4.0-1 [259 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libfftw3-double3 amd64 3.3.5-3 [731 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libxcursor1 amd64 1:1.1.14-1+deb9u2 [34.9 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libxinerama1 amd64 2:1.1.3-1+b3 [16.7 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libfltk1.3 amd64 1.3.4-4 [550 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libnuma1 amd64 2.0.11-2.1 [33.3 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libpciaccess0 amd64 0.13.4-1+b2 [50.0 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 librelion+mpi+gui-1.4-1 amd64 1.4+dfsg-2+b2 [701 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libhwloc5 amd64 1.11.5-1 [105 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 ocl-icd-libopencl1 amd64 2.2.11-1 [36.8 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libhwloc-plugins amd64 1.11.5-1 [16.1 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libopenmpi2 amd64 2.0.2-2 [2008 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 openmpi-common all 2.0.2-2 [149 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 openmpi-bin amd64 2.0.2-2 [186 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 relion-bin+mpi+gui amd64 1.4+dfsg-2+b2 [245 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 xml-core all 0.17 [23.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.1 MB in 0s (40.3 MB/s) Selecting previously unselected package libxau6: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 ... 4411 files and directories currently installed.) Preparing to unpack .../00-libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package libicu57:amd64. Preparing to unpack .../02-libicu57_57.1-6+deb9u4_amd64.deb ... Unpacking libicu57:amd64 (57.1-6+deb9u4) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../03-libxml2_2.9.4+dfsg1-2.2+deb9u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Selecting previously unselected package ucf. Preparing to unpack .../04-ucf_3.0036_all.deb ... Moving old data out of the way Unpacking ucf (3.0036) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../05-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../06-fontconfig-config_2.11.0-6.7_all.deb ... Unpacking fontconfig-config (2.11.0-6.7) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../07-libbsd0_0.8.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.8.3-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../08-libexpat1_2.2.0-2+deb9u3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-2+deb9u3) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../09-libnl-3-200_3.2.27-2_amd64.deb ... Unpacking libnl-3-200:amd64 (3.2.27-2) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../10-libnl-route-3-200_3.2.27-2_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.2.27-2) ... Selecting previously unselected package libibverbs1. Preparing to unpack .../11-libibverbs1_1.2.1-2_amd64.deb ... Unpacking libibverbs1 (1.2.1-2) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../12-libpsm-infinipath1_3.3+19.g67c0807.open-3_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Selecting previously unselected package librdmacm1. Preparing to unpack .../13-librdmacm1_1.1.0-2_amd64.deb ... Unpacking librdmacm1 (1.1.0-2) ... Selecting previously unselected package libfabric1. 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Preparing to unpack .../37-libhwloc5_1.11.5-1_amd64.deb ... Unpacking libhwloc5:amd64 (1.11.5-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../38-ocl-icd-libopencl1_2.2.11-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.2.11-1) ... Selecting previously unselected package libhwloc-plugins. Preparing to unpack .../39-libhwloc-plugins_1.11.5-1_amd64.deb ... Unpacking libhwloc-plugins (1.11.5-1) ... Selecting previously unselected package libopenmpi2:amd64. Preparing to unpack .../40-libopenmpi2_2.0.2-2_amd64.deb ... Unpacking libopenmpi2:amd64 (2.0.2-2) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../41-openmpi-common_2.0.2-2_all.deb ... Unpacking openmpi-common (2.0.2-2) ... Selecting previously unselected package openmpi-bin. Preparing to unpack .../42-openmpi-bin_2.0.2-2_amd64.deb ... Unpacking openmpi-bin (2.0.2-2) ... Selecting previously unselected package relion-bin+mpi+gui. Preparing to unpack .../43-relion-bin+mpi+gui_1.4+dfsg-2+b2_amd64.deb ... Unpacking relion-bin+mpi+gui (1.4+dfsg-2+b2) ... Selecting previously unselected package xml-core. Preparing to unpack .../44-xml-core_0.17_all.deb ... Unpacking xml-core (0.17) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libpng16-16:amd64 (1.6.28-1+deb9u1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libnuma1:amd64 (2.0.11-2.1) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up sgml-base (1.29) ... Setting up libfftw3-double3:amd64 (3.3.5-3) ... Setting up libicu57:amd64 (57.1-6+deb9u4) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Setting up libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Setting up openmpi-common (2.0.2-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libpciaccess0:amd64 (0.13.4-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up xml-core (0.17) ... Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ... Setting up libnl-3-200:amd64 (3.2.27-2) ... Setting up libx11-data (2:1.6.4-3+deb9u1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up libnl-route-3-200:amd64 (3.2.27-2) ... Setting up libhwloc5:amd64 (1.11.5-1) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up libibverbs1 (1.2.1-2) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up librdmacm1 (1.1.0-2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libfabric1 (1.4.0-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Setting up libopenmpi2:amd64 (2.0.2-2) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ... Setting up openmpi-bin (2.0.2-2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up libfltk1.3:amd64 (1.3.4-4) ... Setting up librelion+mpi+gui-1.4-1:amd64 (1.4+dfsg-2+b2) ... Setting up relion-bin+mpi+gui (1.4+dfsg-2+b2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for sgml-base (1.29) ... 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', '-y', 'install', 'relion-bin+mpi+gui=1.4+dfsg-2+b2'] 0m10.0s INFO: Running scripts post_install 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_install_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_install_exceptions'] 0m10.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m11.1s DEBUG: No broken symlinks as far as we can find. 0m11.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', '-ac', '--ignore-obsolete'] 0m12.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', '-ac', '--ignore-obsolete'] 0m12.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.1s DUMP: 0.15.6 0m12.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m12.1s INFO: Running adequate version 0.15.6 now. 0m12.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'relion-bin+mpi+gui'] 0m12.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'relion-bin+mpi+gui'] 0m12.6s INFO: Running scripts pre_remove 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_exceptions'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/pre_remove_exceptions'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.0s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed fontconfig-config fontconfig-config 2.11.0-6.7 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbsd0:amd64 libbsd0 0.8.3-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u3 install ok installed libfabric1 libfabric1 1.4.0-1 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.5-3 install ok installed libfltk1.3:amd64 libfltk1.3 1.3.4-4 install ok installed libfontconfig1:amd64 libfontconfig1 2.11.0-6.7+b1 install ok installed libfreetype6:amd64 libfreetype6 2.6.3-3.2+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgomp1:amd64 libgomp1 6.3.0-18+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libhwloc-plugins libhwloc-plugins 1.11.5-1 install ok installed libhwloc5:amd64 libhwloc5 1.11.5-1 install ok installed libibverbs1 libibverbs1 1.2.1-2 install ok installed libicu57:amd64 libicu57 57.1-6+deb9u4 install ok installed libltdl7:amd64 libltdl7 2.4.6-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnl-3-200:amd64 libnl-3-200 3.2.27-2 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.2.27-2 install ok installed libnuma1:amd64 libnuma1 2.0.11-2.1 install ok installed libopenmpi2:amd64 libopenmpi2 2.0.2-2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpciaccess0:amd64 libpciaccess0 0.13.4-1+b2 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpng16-16:amd64 libpng16-16 1.6.28-1+deb9u1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+19.g67c0807.open-3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed librdmacm1 librdmacm1 1.1.0-2 install ok installed librelion+mpi+gui-1.4-1:amd64 librelion+mpi+gui-1.4-1 1.4+dfsg-2+b2 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed libx11-6:amd64 libx11-6 2:1.6.4-3+deb9u1 install ok installed libx11-data libx11-data 2:1.6.4-3+deb9u1 install ok installed libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.1.14-1+deb9u2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxfixes3:amd64 libxfixes3 1:5.0.3-1 install ok installed libxft2:amd64 libxft2 2.3.2-1+b2 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.3-1+b3 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-2.2+deb9u2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.2.11-1 install ok installed openmpi-bin openmpi-bin 2.0.2-2 install ok installed openmpi-common openmpi-common 2.0.2-2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed relion-bin+mpi+gui relion-bin+mpi+gui 1.4+dfsg-2+b2 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sgml-base sgml-base 1.29 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed ucf ucf 3.0036 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed xml-core xml-core 0.17 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'libbsd0:amd64', 'libexpat1:amd64', 'libfabric1', 'libfftw3-double3:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran3:amd64', 'libgomp1:amd64', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libicu57:amd64', 'libltdl7:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi2:amd64', 'libpciaccess0:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libquadmath0:amd64', 'librdmacm1', 'librelion+mpi+gui-1.4-1:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'sgml-base', 'ucf', 'xml-core', 'relion-bin+mpi+gui'] 0m15.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fontconfig-config fonts-dejavu-core libbsd0 libexpat1 libfabric1 libfftw3-double3 libfltk1.3 libfontconfig1 libfreetype6 libgfortran3 libgomp1 libhwloc-plugins libhwloc5 libibverbs1 libicu57 libltdl7 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi2 libpciaccess0 libpng16-16 libpsm-infinipath1 libquadmath0 librdmacm1 librelion+mpi+gui-1.4-1 libx11-6 libx11-data libxau6 libxcb1 libxcursor1 libxdmcp6 libxext6 libxfixes3 libxft2 libxinerama1 libxml2 libxrender1 ocl-icd-libopencl1 openmpi-bin openmpi-common relion-bin+mpi+gui sgml-base ucf xml-core 0 upgraded, 0 newly installed, 45 to remove and 0 not upgraded. After this operation, 64.0 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5511 files and directories currently installed.) Removing relion-bin+mpi+gui (1.4+dfsg-2+b2) ... Removing librelion+mpi+gui-1.4-1:amd64 (1.4+dfsg-2+b2) ... Removing libfltk1.3:amd64 (1.3.4-4) ... Removing libxft2:amd64 (2.3.2-1+b2) ... Removing libfontconfig1:amd64 (2.11.0-6.7+b1) ... Removing fontconfig-config (2.11.0-6.7) ... Removing fonts-dejavu-core (2.37-1) ... Removing libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing openmpi-bin (2.0.2-2) ... Removing libopenmpi2:amd64 (2.0.2-2) ... Removing libfabric1 (1.4.0-1) ... Removing libfftw3-double3:amd64 (3.3.5-3) ... Removing libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libhwloc-plugins (1.11.5-1) ... Removing libhwloc5:amd64 (1.11.5-1) ... Removing librdmacm1 (1.1.0-2) ... Removing libibverbs1 (1.2.1-2) ... Removing libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Removing libicu57:amd64 (57.1-6+deb9u4) ... Removing libltdl7:amd64 (2.4.6-2) ... Removing libnl-route-3-200:amd64 (3.2.27-2) ... Removing libnl-3-200:amd64 (3.2.27-2) ... Removing libnuma1:amd64 (2.0.11-2.1) ... Removing libpciaccess0:amd64 (0.13.4-1+b2) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libxinerama1:amd64 (2:1.1.3-1+b3) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxfixes3:amd64 (1:5.0.3-1) ... Removing ocl-icd-libopencl1:amd64 (2.2.11-1) ... Removing openmpi-common (2.0.2-2) ... Removing xml-core (0.17) ... Removing sgml-base (1.29) ... Removing ucf (3.0036) ... Removing libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Removing libxcb1:amd64 (1.12-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.8.3-1) ... Removing libx11-data (2:1.6.4-3+deb9u1) ... Removing libxau6:amd64 (1:1.0.8-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'libbsd0:amd64', 'libexpat1:amd64', 'libfabric1', 'libfftw3-double3:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran3:amd64', 'libgomp1:amd64', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libicu57:amd64', 'libltdl7:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi2:amd64', 'libpciaccess0:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libquadmath0:amd64', 'librdmacm1', 'librelion+mpi+gui-1.4-1:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'sgml-base', 'ucf', 'xml-core', 'relion-bin+mpi+gui'] 0m15.1s INFO: Running scripts post_remove 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_remove_exceptions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_remove_exceptions'] 0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'libbsd0:amd64', 'libexpat1:amd64', 'libfabric1', 'libfftw3-double3:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran3:amd64', 'libgomp1:amd64', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libicu57:amd64', 'libltdl7:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi2:amd64', 'libpciaccess0:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libquadmath0:amd64', 'librdmacm1', 'librelion+mpi+gui-1.4-1:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'sgml-base', 'ucf', 'xml-core'] 0m15.6s DUMP: (Reading database ... 4441 files and directories currently installed.) Purging configuration files for fontconfig-config (2.11.0-6.7) ... Purging configuration files for fonts-dejavu-core (2.37-1) ... dpkg: warning: ignoring request to remove libbsd0 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 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 libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc5 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu57 which isn't installed dpkg: warning: ignoring request to remove libltdl7 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.2.27-2) ... 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 libopenmpi2 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsm-infinipath1 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove librdmacm1 which isn't installed dpkg: warning: ignoring request to remove librelion+mpi+gui-1.4-1 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 Purging configuration files for libxau6:amd64 (1:1.0.8-1) ... 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 libxrender1 which isn't installed dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openmpi-bin (2.0.2-2) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for sgml-base (1.29) ... Purging configuration files for ucf (3.0036) ... Purging configuration files for xml-core (0.17) ... 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'libbsd0:amd64', 'libexpat1:amd64', 'libfabric1', 'libfftw3-double3:amd64', 'libfltk1.3:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran3:amd64', 'libgomp1:amd64', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libicu57:amd64', 'libltdl7:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi2:amd64', 'libpciaccess0:amd64', 'libpng16-16:amd64', 'libpsm-infinipath1', 'libquadmath0:amd64', 'librdmacm1', 'librelion+mpi+gui-1.4-1:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxcursor1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'sgml-base', 'ucf', 'xml-core'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', 'relion-bin+mpi+gui'] 0m15.6s DUMP: dpkg: warning: ignoring request to remove relion-bin+mpi+gui which isn't installed 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', 'relion-bin+mpi+gui'] 0m15.6s INFO: Running scripts post_purge 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_purge_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_purge_exceptions'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', '--pending'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--purge', '--pending'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--remove', '--pending'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg', '--remove', '--pending'] 0m15.6s INFO: Running scripts post_test 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_test_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'tmp/scripts/post_test_exceptions'] 0m15.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m15.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m16.3s DEBUG: No broken symlinks as far as we can find. 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-divert', '--list'] 0m16.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'dpkg-divert', '--list'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'clean'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7', 'apt-get', 'clean'] 0m16.3s DEBUG: Recording chroot state 0m16.7s INFO: PASS: Installation and purging test. 0m16.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/shm'] 0m16.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/shm'] 0m16.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/console'] 0m17.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/console'] 0m17.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/ptmx'] 0m17.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/ptmx'] 0m17.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts'] 0m17.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/dev/pts'] 0m17.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/proc'] 0m17.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7/proc'] 0m17.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m17.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpx3r5tin7'] 0m17.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpx3r5tin7 0m17.1s INFO: PASS: All tests. 0m17.1s INFO: piuparts run ends. ret=0 End: 2023-03-25 23:49:55 GMT