Start: 2022-09-16 07:50:12 GMT [jessie] Package: relion-bin Source: relion Version: 1.3+dfsg-2 Installed-Size: 844 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libfftw3-double3, libgcc1 (>= 1:4.1.1), librelion-1.3-1, libstdc++6 (>= 4.9) Conflicts: relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: 11b37d59596139388bb1a837e1e09405 Section: science Priority: optional Filename: pool/main/r/relion/relion-bin_1.3+dfsg-2_amd64.deb Size: 171680 MD5sum: 411374dd81de60be45537e5210916aed SHA1: 55cb3d40cfd5d09db5d5a9b4846e9dc1fa3eb483 SHA256: 163b9e44ee86a3197caaef8fdc4f62263cdbbaae2d507bb568bf19e7fdaea4c4 [jessie-lts] Package: relion-bin Source: relion Version: 1.3+dfsg-2 Installed-Size: 844 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libfftw3-double3, libgcc1 (>= 1:4.1.1), librelion-1.3-1, libstdc++6 (>= 4.9) Conflicts: relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description: toolkit for 3D reconstructions in cryo-electron microscopy Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Description-md5: 11b37d59596139388bb1a837e1e09405 Section: science Priority: optional Filename: pool/main/r/relion/relion-bin_1.3+dfsg-2_amd64.deb Size: 171680 MD5sum: 411374dd81de60be45537e5210916aed SHA1: 55cb3d40cfd5d09db5d5a9b4846e9dc1fa3eb483 SHA256: 163b9e44ee86a3197caaef8fdc4f62263cdbbaae2d507bb568bf19e7fdaea4c4 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-jessie --skip-logrotatefiles-test --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d jessie-lts -B /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat --apt relion-bin=1.3+dfsg-2 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 --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-jessie --skip-logrotatefiles-test --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d jessie-lts -B /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat --apt relion-bin=1.3+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpq_8v0jq5 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpq_8v0jq5 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpq_8v0jq5/tmp/scripts/ 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-jessie to /srv/piuparts.debian.org/tmp/tmpq_8v0jq5/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'update'] 0m3.0s DUMP: Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main amd64 Packages Hit http://deb.debian.org jessie/main Translation-en Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.4s DUMP: c58dd1ad19dd97acb5ff8b7cd65de431 - 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.4s INFO: Running scripts post_setup 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_jessie-fake-essential'] 0m4.3s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... The following NEW packages will be installed: init-system-helpers ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 83.7 kB of archives. After this operation, 334 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ jessie/main init-system-helpers all 1.22 [14.0 kB] Get:2 http://deb.debian.org/debian/ jessie/main ucf all 3.0030 [69.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.7 kB in 0s (3704 kB/s) Selecting previously unselected package init-system-helpers. (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 ... 7449 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.22_all.deb ... Unpacking init-system-helpers (1.22) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0030_all.deb ... Moving old data out of the way Unpacking ucf (3.0030) ... Setting up init-system-helpers (1.22) ... Setting up ucf (3.0030) ... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_jessie-fake-essential'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.4s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.4 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u1 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+b1 install ok installed e2fsprogs e2fsprogs 1.42.12-2+b1 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u1 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed init-system-helpers init-system-helpers 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+b3 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+b1 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+b1 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u1 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u7 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u7 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u11 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u7 install ok installed systemd-sysv systemd-sysv 215-17+deb8u7 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u1 install ok installed tzdata tzdata 2018e-0+deb8u1 install ok installed ucf ucf 3.0030 install ok installed udev udev 215-17+deb8u7 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+b1 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat 0m4.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m4.8s INFO: Running scripts is_testable 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s INFO: Running scripts pre_test 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_test_root_password'] 0m4.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_test_root_password'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'show', '--no-all-versions', 'relion-bin'] 0m4.8s DUMP: Package: relion-bin Source: relion Version: 1.3+dfsg-2 Installed-Size: 844 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libfftw3-double3, libgcc1 (>= 1:4.1.1), librelion-1.3-1, libstdc++6 (>= 4.9) Conflicts: relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description-en: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions as well as a C++ API. . relion-bin provides the serial command-line tools Description-md5: 11b37d59596139388bb1a837e1e09405 Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Section: science Priority: optional Filename: pool/main/r/relion/relion-bin_1.3+dfsg-2_amd64.deb Size: 171680 MD5sum: 411374dd81de60be45537e5210916aed SHA1: 55cb3d40cfd5d09db5d5a9b4846e9dc1fa3eb483 SHA256: 163b9e44ee86a3197caaef8fdc4f62263cdbbaae2d507bb568bf19e7fdaea4c4 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'show', '--no-all-versions', 'relion-bin'] 0m4.8s INFO: apt-cache knows about the following packages: relion-bin 0m4.8s INFO: Running scripts pre_install 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m4.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m5.0s DUMP: relion-bin: Installed: (none) Candidate: 1.3+dfsg-2 Version table: 1.3+dfsg-2 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin'] 0m5.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libfftw3-double3 libgomp1 librelion-1.3-1 Suggested packages: libfftw3-bin libfftw3-dev The following NEW packages will be installed: libfftw3-double3 libgomp1 librelion-1.3-1 relion-bin 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 1489 kB of archives. After this operation, 4919 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ jessie/main libgomp1 amd64 4.9.2-10+deb8u1 [37.8 kB] Get:2 http://deb.debian.org/debian/ jessie/main libfftw3-double3 amd64 3.3.4-2 [722 kB] Get:3 http://deb.debian.org/debian/ jessie/main librelion-1.3-1 amd64 1.3+dfsg-2 [557 kB] Get:4 http://deb.debian.org/debian/ jessie/main relion-bin amd64 1.3+dfsg-2 [172 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1489 kB in 0s (25.2 MB/s) Selecting previously unselected package libgomp1: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 ... 7475 files and directories currently installed.) Preparing to unpack .../libgomp1_4.9.2-10+deb8u1_amd64.deb ... Unpacking libgomp1:amd64 (4.9.2-10+deb8u1) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../libfftw3-double3_3.3.4-2_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.4-2) ... Selecting previously unselected package librelion-1.3-1:amd64. Preparing to unpack .../librelion-1.3-1_1.3+dfsg-2_amd64.deb ... Unpacking librelion-1.3-1:amd64 (1.3+dfsg-2) ... Selecting previously unselected package relion-bin. Preparing to unpack .../relion-bin_1.3+dfsg-2_amd64.deb ... Unpacking relion-bin (1.3+dfsg-2) ... Setting up libgomp1:amd64 (4.9.2-10+deb8u1) ... Setting up libfftw3-double3:amd64 (3.3.4-2) ... Setting up librelion-1.3-1:amd64 (1.3+dfsg-2) ... Setting up relion-bin (1.3+dfsg-2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin'] 0m5.7s INFO: Running scripts post_install 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m5.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m6.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m6.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpq_8v0jq5 to jessie-lts 0m6.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main deb http://security.debian.org jessie/updates main 0m6.0s INFO: Running scripts pre_distupgrade 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'update'] 0m7.8s DUMP: Get:1 http://security.debian.org jessie/updates InRelease [44.9 kB] Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Get:2 http://security.debian.org jessie/updates/main amd64 Packages [781 kB] Hit http://deb.debian.org jessie/main amd64 Packages Hit http://deb.debian.org jessie/main Translation-en Get:3 http://security.debian.org jessie/updates/main Translation-en [401 kB] Fetched 1227 kB in 0s (1532 kB/s) Reading package lists... 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'update'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-yf', 'dist-upgrade'] 0m11.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt bash e2fslibs e2fsprogs gcc-4.9-base libapt-pkg4.12 libbz2-1.0 libcomerr2 libgcc1 libgcrypt20 libgomp1 libss2 libstdc++6 libsystemd0 libudev1 perl-base systemd systemd-sysv tar tzdata udev zlib1g 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 10.9 MB of archives. After this operation, 3840 kB of additional disk space will be used. Get:1 http://security.debian.org/ jessie/updates/main bash amd64 4.3-11+deb8u2 [1173 kB] Get:2 http://security.debian.org/ jessie/updates/main e2fslibs amd64 1.42.12-2+deb8u2 [186 kB] Get:3 http://security.debian.org/ jessie/updates/main e2fsprogs amd64 1.42.12-2+deb8u2 [751 kB] Get:4 http://security.debian.org/ jessie/updates/main perl-base amd64 5.20.2-3+deb8u12 [1231 kB] Get:5 http://security.debian.org/ jessie/updates/main tar amd64 1.27.1-2+deb8u2 [676 kB] Get:6 http://security.debian.org/ jessie/updates/main libbz2-1.0 amd64 1.0.6-7+deb8u2 [43.3 kB] Get:7 http://security.debian.org/ jessie/updates/main libgomp1 amd64 4.9.2-10+deb8u2 [37.8 kB] Get:8 http://security.debian.org/ jessie/updates/main gcc-4.9-base amd64 4.9.2-10+deb8u2 [160 kB] Get:9 http://security.debian.org/ jessie/updates/main libgcc1 amd64 1:4.9.2-10+deb8u2 [39.4 kB] Get:10 http://security.debian.org/ jessie/updates/main libstdc++6 amd64 4.9.2-10+deb8u2 [273 kB] Get:11 http://security.debian.org/ jessie/updates/main zlib1g amd64 1:1.2.8.dfsg-2+deb8u1 [88.3 kB] Get:12 http://security.debian.org/ jessie/updates/main libapt-pkg4.12 amd64 1.0.9.8.6 [794 kB] Get:13 http://security.debian.org/ jessie/updates/main apt amd64 1.0.9.8.6 [1109 kB] Get:14 http://security.debian.org/ jessie/updates/main libudev1 amd64 215-17+deb8u13 [58.8 kB] Get:15 http://security.debian.org/ jessie/updates/main udev amd64 215-17+deb8u13 [878 kB] Get:16 http://security.debian.org/ jessie/updates/main libcomerr2 amd64 1.42.12-2+deb8u2 [60.6 kB] Get:17 http://security.debian.org/ jessie/updates/main libss2 amd64 1.42.12-2+deb8u2 [64.9 kB] Get:18 http://security.debian.org/ jessie/updates/main libgcrypt20 amd64 1.6.3-2+deb8u8 [394 kB] Get:19 http://security.debian.org/ jessie/updates/main libsystemd0 amd64 215-17+deb8u13 [90.5 kB] Get:20 http://security.debian.org/ jessie/updates/main systemd amd64 215-17+deb8u13 [2555 kB] Get:21 http://security.debian.org/ jessie/updates/main systemd-sysv amd64 215-17+deb8u13 [37.5 kB] Get:22 http://security.debian.org/ jessie/updates/main tzdata all 2019c-0+deb8u1 [234 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.9 MB in 0s (41.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7520 files and directories currently installed.) Preparing to unpack .../bash_4.3-11+deb8u2_amd64.deb ... Unpacking bash (4.3-11+deb8u2) over (4.3-11+deb8u1) ... Setting up bash (4.3-11+deb8u2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 7520 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.42.12-2+deb8u2_amd64.deb ... Unpacking e2fslibs:amd64 (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up e2fslibs:amd64 (1.42.12-2+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7519 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.12-2+deb8u2_amd64.deb ... Unpacking e2fsprogs (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up e2fsprogs (1.42.12-2+deb8u2) ... (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 ... 7518 files and directories currently installed.) Preparing to unpack .../perl-base_5.20.2-3+deb8u12_amd64.deb ... Unpacking perl-base (5.20.2-3+deb8u12) over (5.20.2-3+deb8u11) ... Setting up perl-base (5.20.2-3+deb8u12) ... (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 ... 7518 files and directories currently installed.) Preparing to unpack .../tar_1.27.1-2+deb8u2_amd64.deb ... Unpacking tar (1.27.1-2+deb8u2) over (1.27.1-2+deb8u1) ... Setting up tar (1.27.1-2+deb8u2) ... (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 ... 7518 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.6-7+deb8u2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.6-7+deb8u2) over (1.0.6-7+b3) ... Setting up libbz2-1.0:amd64 (1.0.6-7+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7517 files and directories currently installed.) Preparing to unpack .../libgomp1_4.9.2-10+deb8u2_amd64.deb ... Unpacking libgomp1:amd64 (4.9.2-10+deb8u2) over (4.9.2-10+deb8u1) ... Preparing to unpack .../gcc-4.9-base_4.9.2-10+deb8u2_amd64.deb ... Unpacking gcc-4.9-base:amd64 (4.9.2-10+deb8u2) over (4.9.2-10+deb8u1) ... Setting up gcc-4.9-base:amd64 (4.9.2-10+deb8u2) ... (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 ... 7517 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a4.9.2-10+deb8u2_amd64.deb ... Unpacking libgcc1:amd64 (1:4.9.2-10+deb8u2) over (1:4.9.2-10+deb8u1) ... Setting up libgcc1:amd64 (1:4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7517 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.9.2-10+deb8u2_amd64.deb ... Unpacking libstdc++6:amd64 (4.9.2-10+deb8u2) over (4.9.2-10+deb8u1) ... Setting up libstdc++6:amd64 (4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7517 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-2+deb8u1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.8.dfsg-2+deb8u1) over (1:1.2.8.dfsg-2+b1) ... Setting up zlib1g:amd64 (1:1.2.8.dfsg-2+deb8u1) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7516 files and directories currently installed.) Preparing to unpack .../libapt-pkg4.12_1.0.9.8.6_amd64.deb ... Unpacking libapt-pkg4.12:amd64 (1.0.9.8.6) over (1.0.9.8.4) ... Setting up libapt-pkg4.12:amd64 (1.0.9.8.6) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7516 files and directories currently installed.) Preparing to unpack .../apt_1.0.9.8.6_amd64.deb ... Unpacking apt (1.0.9.8.6) over (1.0.9.8.4) ... Setting up apt (1.0.9.8.6) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7516 files and directories currently installed.) Preparing to unpack .../libudev1_215-17+deb8u13_amd64.deb ... Unpacking libudev1:amd64 (215-17+deb8u13) over (215-17+deb8u7) ... Setting up libudev1:amd64 (215-17+deb8u13) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7516 files and directories currently installed.) Preparing to unpack .../udev_215-17+deb8u13_amd64.deb ... Unpacking udev (215-17+deb8u13) over (215-17+deb8u7) ... Processing triggers for systemd (215-17+deb8u7) ... Setting up udev (215-17+deb8u13) ... addgroup: The group `input' already exists as a system group. Exiting. A chroot environment has been detected, udev not started. A chroot environment has been detected, udev not started. (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 ... 7516 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.12-2+deb8u2_amd64.deb ... Unpacking libcomerr2:amd64 (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up libcomerr2:amd64 (1.42.12-2+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7515 files and directories currently installed.) Preparing to unpack .../libss2_1.42.12-2+deb8u2_amd64.deb ... Unpacking libss2:amd64 (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up libss2:amd64 (1.42.12-2+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7514 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.3-2+deb8u8_amd64.deb ... Unpacking libgcrypt20:amd64 (1.6.3-2+deb8u8) over (1.6.3-2+deb8u4) ... Setting up libgcrypt20:amd64 (1.6.3-2+deb8u8) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7514 files and directories currently installed.) Preparing to unpack .../libsystemd0_215-17+deb8u13_amd64.deb ... Unpacking libsystemd0:amd64 (215-17+deb8u13) over (215-17+deb8u7) ... Setting up libsystemd0:amd64 (215-17+deb8u13) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7514 files and directories currently installed.) Preparing to unpack .../systemd_215-17+deb8u13_amd64.deb ... Unpacking systemd (215-17+deb8u13) over (215-17+deb8u7) ... Setting up systemd (215-17+deb8u13) ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (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 ... 7514 files and directories currently installed.) Preparing to unpack .../systemd-sysv_215-17+deb8u13_amd64.deb ... Unpacking systemd-sysv (215-17+deb8u13) over (215-17+deb8u7) ... Setting up systemd-sysv (215-17+deb8u13) ... (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 ... 7514 files and directories currently installed.) Preparing to unpack .../tzdata_2019c-0+deb8u1_all.deb ... Unpacking tzdata (2019c-0+deb8u1) over (2018e-0+deb8u1) ... Setting up tzdata (2019c-0+deb8u1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 16 07:50:23 UTC 2022. Universal Time is now: Fri Sep 16 07:50:23 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgomp1:amd64 (4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-yf', 'dist-upgrade'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m11.7s DUMP: ea587cb5da6f95fbc79bf1681671e909 - 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'show', '--no-all-versions', 'relion-bin'] 0m11.7s DUMP: Package: relion-bin Source: relion Version: 1.3+dfsg-2 Installed-Size: 844 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libfftw3-double3, libgcc1 (>= 1:4.1.1), librelion-1.3-1, libstdc++6 (>= 4.9) Conflicts: relion-bin+gui, relion-bin+mpi, relion-bin+mpi+gui Description-en: toolkit for 3D reconstructions in cryo-electron microscopy RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. . RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions as well as a C++ API. . relion-bin provides the serial command-line tools Description-md5: 11b37d59596139388bb1a837e1e09405 Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Section: science Priority: optional Filename: pool/main/r/relion/relion-bin_1.3+dfsg-2_amd64.deb Size: 171680 MD5sum: 411374dd81de60be45537e5210916aed SHA1: 55cb3d40cfd5d09db5d5a9b4846e9dc1fa3eb483 SHA256: 163b9e44ee86a3197caaef8fdc4f62263cdbbaae2d507bb568bf19e7fdaea4c4 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'show', '--no-all-versions', 'relion-bin'] 0m11.7s INFO: apt-cache knows about the following packages: relion-bin 0m11.7s INFO: Running scripts pre_install 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m11.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ jessie/updates/main Translation-en 500 http://security.debian.org/ jessie/updates/main amd64 Packages release v=8,o=Debian,a=oldoldstable,n=jessie,l=Debian-Security,c=main origin security.debian.org 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m11.8s DUMP: relion-bin: Installed: 1.3+dfsg-2 Candidate: 1.3+dfsg-2 Version table: *** 1.3+dfsg-2 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 100 /var/lib/dpkg/status 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin'] 0m12.0s DUMP: Reading package lists... Building dependency tree... Reading state information... relion-bin is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin'] 0m12.0s INFO: Running scripts post_install 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m12.0s INFO: Running scripts post_distupgrade 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m12.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m12.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m12.7s INFO: Running scripts pre_install 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_database-server'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_exceptions'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_extras'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m12.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ jessie/updates/main Translation-en 500 http://security.debian.org/ jessie/updates/main amd64 Packages release v=8,o=Debian,a=oldoldstable,n=jessie,l=Debian-Security,c=main origin security.debian.org 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m12.8s DUMP: relion-bin: Installed: 1.3+dfsg-2 Candidate: 1.3+dfsg-2 Version table: *** 1.3+dfsg-2 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 100 /var/lib/dpkg/status 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-cache', 'policy', 'relion-bin'] 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin=1.3+dfsg-2'] 0m13.0s DUMP: Reading package lists... Building dependency tree... Reading state information... relion-bin is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', '-y', 'install', 'relion-bin=1.3+dfsg-2'] 0m13.0s INFO: Running scripts post_install 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_install_exceptions'] 0m13.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m13.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m13.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', '-ac', '--ignore-obsolete'] 0m14.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', '-ac', '--ignore-obsolete'] 0m14.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.2s DUMP: 0.15.6 0m14.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m14.2s INFO: Running adequate version 0.15.6 now. 0m14.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'relion-bin'] 0m14.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'relion-bin'] 0m14.5s INFO: Running scripts pre_remove 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_exceptions'] 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/pre_remove_exceptions'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m15.5s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.6 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u2 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+deb8u2 install ok installed e2fsprogs e2fsprogs 1.42.12-2+deb8u2 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u2 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed init-system-helpers init-system-helpers 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.6 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+deb8u2 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+deb8u2 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libfftw3-double3:amd64 libfftw3-double3 3.3.4-2 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u2 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u8 install ok installed libgomp1:amd64 libgomp1 4.9.2-10+deb8u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed librelion-1.3-1:amd64 librelion-1.3-1 1.3+dfsg-2 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+deb8u2 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u2 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u13 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u13 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u12 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed relion-bin relion-bin 1.3+dfsg-2 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u13 install ok installed systemd-sysv systemd-sysv 215-17+deb8u13 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u2 install ok installed tzdata tzdata 2019c-0+deb8u1 install ok installed ucf ucf 3.0030 install ok installed udev udev 215-17+deb8u13 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+deb8u1 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'remove', 'libfftw3-double3:amd64', 'libgomp1:amd64', 'librelion-1.3-1:amd64', 'relion-bin'] 0m15.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libfftw3-double3 libgomp1 librelion-1.3-1 relion-bin 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. After this operation, 4919 kB 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 ... 7517 files and directories currently installed.) Removing relion-bin (1.3+dfsg-2) ... Removing librelion-1.3-1:amd64 (1.3+dfsg-2) ... Removing libfftw3-double3:amd64 (3.3.4-2) ... Removing libgomp1:amd64 (4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'remove', 'libfftw3-double3:amd64', 'libgomp1:amd64', 'librelion-1.3-1:amd64', 'relion-bin'] 0m15.9s INFO: Running scripts post_remove 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_remove_exceptions'] 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_remove_exceptions'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', 'libfftw3-double3:amd64', 'libgomp1:amd64', 'librelion-1.3-1:amd64'] 0m15.9s DUMP: (Reading database ... 7472 files and directories currently installed.) Removing libfftw3-double3:amd64 (3.3.4-2) ... Purging configuration files for libfftw3-double3:amd64 (3.3.4-2) ... Removing libgomp1:amd64 (4.9.2-10+deb8u2) ... Purging configuration files for libgomp1:amd64 (4.9.2-10+deb8u2) ... Removing librelion-1.3-1:amd64 (1.3+dfsg-2) ... Purging configuration files for librelion-1.3-1:amd64 (1.3+dfsg-2) ... 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', 'libfftw3-double3:amd64', 'libgomp1:amd64', 'librelion-1.3-1:amd64'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', 'relion-bin'] 0m15.9s DUMP: dpkg: warning: ignoring request to remove relion-bin which isn't installed 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', 'relion-bin'] 0m15.9s INFO: Running scripts post_purge 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_purge_exceptions'] 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_purge_exceptions'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', '--pending'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--purge', '--pending'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--remove', '--pending'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'dpkg', '--remove', '--pending'] 0m16.0s INFO: Running scripts post_test 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_test_exceptions'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'tmp/scripts/post_test_exceptions'] 0m16.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m16.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', '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/tmpq_8v0jq5', 'dpkg-divert', '--list'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'clean'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5', 'apt-get', 'clean'] 0m16.4s DEBUG: Recording chroot state 0m17.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/shm'] 0m17.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/shm'] 0m17.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/console'] 0m17.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/console'] 0m17.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/ptmx'] 0m17.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/ptmx'] 0m17.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts'] 0m17.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/dev/pts'] 0m17.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/proc'] 0m17.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5/proc'] 0m17.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m17.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpq_8v0jq5'] 0m17.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpq_8v0jq5 0m17.3s INFO: PASS: Upgrading between Debian distributions. 0m17.3s INFO: PASS: All tests. 0m17.3s INFO: piuparts run ends. ret=0 End: 2022-09-16 07:50:29 GMT