Start: 2018-09-29 02:05:37 UTC [stretch] Package: disulfinder Version: 1.2.11-6 Installed-Size: 726 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), disulfinder-data Description: cysteines disulfide bonding state and connectivity predictor Homepage: http://disulfind.dsi.unifi.it/ Description-md5: 5f70380c76687c70f279559ee87b7d0e Tag: role::program Section: science Priority: extra Filename: pool/main/d/disulfinder/disulfinder_1.2.11-6_amd64.deb Size: 260686 MD5sum: 1e656f40725e9e28843c52dfc1334e4d SHA256: e047cb1432c30e46fe3e37b6ff7601489b4c8913ba6c3d4789fc6a0967599f6f [stretch-proposed] Package: disulfinder Version: 1.2.11-6 Installed-Size: 726 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), disulfinder-data Description: cysteines disulfide bonding state and connectivity predictor Homepage: http://disulfind.dsi.unifi.it/ Description-md5: 5f70380c76687c70f279559ee87b7d0e Tag: role::program Section: science Priority: extra Filename: pool/main/d/disulfinder/disulfinder_1.2.11-6_amd64.deb Size: 260686 MD5sum: 1e656f40725e9e28843c52dfc1334e4d SHA256: e047cb1432c30e46fe3e37b6ff7601489b4c8913ba6c3d4789fc6a0967599f6f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://mirror-ubc.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 -d stretch-proposed -B reference-chroot-metadata.dat --apt disulfinder=1.2.11-6 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 0.93~201809241020~0.92-22-g1ffcf128 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://mirror-ubc.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 -d stretch-proposed -B reference-chroot-metadata.dat --apt disulfinder=1.2.11-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.9.0-8-amd64 #1 SMP Debian 4.9.110-3+deb9u4 (2018-08-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpKYPcX_ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpKYPcX_ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/ptmx'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/ptmx'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/console'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/console'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/shm'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/shm'] 0m2.4s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ stretch main 0m2.4s DEBUG: Created policy-rc.d and chmodded it. 0m2.4s DEBUG: Created resolv.conf. 0m2.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpKYPcX_/tmp/scripts/ 0m2.4s INFO: Running scripts post_chroot_unpack 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'update'] 0m3.5s DUMP: Ign:1 http://mirror-ubc.debian.org/debian stretch InRelease Hit:2 http://mirror-ubc.debian.org/debian stretch Release Reading package lists... 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'update'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.3s DUMP: a904588dbe641b9875f9294ac6279634 - 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.3s INFO: Running scripts post_setup 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.8 install ok installed base-files base-files 9.9+deb9u5 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 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 install ok installed e2fsprogs e2fsprogs 1.43.4-2 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~deb9u2 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 1.4.8 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+deb9u3 install ok installed libc6:amd64 libc6 2.24-11+deb9u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2 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 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u4 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u4 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+deb9u3 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+deb9u4 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 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m5.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m5.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m5.9s INFO: Running scripts is_testable 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s INFO: Running scripts pre_test 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_test_root_password'] 0m5.9s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_test_root_password'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'show', '--no-all-versions', 'disulfinder'] 0m6.1s DUMP: Package: disulfinder Version: 1.2.11-6 Installed-Size: 726 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), disulfinder-data Description-en: cysteines disulfide bonding state and connectivity predictor 'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. . 'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern. Description-md5: 5f70380c76687c70f279559ee87b7d0e Homepage: http://disulfind.dsi.unifi.it/ Tag: role::program Section: science Priority: extra Filename: pool/main/d/disulfinder/disulfinder_1.2.11-6_amd64.deb Size: 260686 MD5sum: 1e656f40725e9e28843c52dfc1334e4d SHA256: e047cb1432c30e46fe3e37b6ff7601489b4c8913ba6c3d4789fc6a0967599f6f 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'show', '--no-all-versions', 'disulfinder'] 0m6.1s INFO: apt-cache knows about the following packages: disulfinder 0m6.1s INFO: Running scripts pre_install 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m6.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages release v=9.5,o=Debian,a=stable,n=stretch,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m6.2s DUMP: disulfinder: Installed: (none) Candidate: 1.2.11-6 Version table: 1.2.11-6 500 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder'] 0m7.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: disulfinder-data The following NEW packages will be installed: disulfinder disulfinder-data 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 1389 kB of archives. After this operation, 13.6 MB of additional disk space will be used. Get:1 http://mirror-ubc.debian.org/debian stretch/main amd64 disulfinder-data all 1.2.11-6 [1129 kB] Get:2 http://mirror-ubc.debian.org/debian stretch/main amd64 disulfinder amd64 1.2.11-6 [261 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1389 kB in 0s (19.5 MB/s) Selecting previously unselected package disulfinder-data. (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 ... 4410 files and directories currently installed.) Preparing to unpack .../disulfinder-data_1.2.11-6_all.deb ... Unpacking disulfinder-data (1.2.11-6) ... Selecting previously unselected package disulfinder. Preparing to unpack .../disulfinder_1.2.11-6_amd64.deb ... Unpacking disulfinder (1.2.11-6) ... Setting up disulfinder-data (1.2.11-6) ... Setting up disulfinder (1.2.11-6) ... 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder'] 0m7.3s INFO: Running scripts post_install 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m7.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m7.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpKYPcX_ to stretch-proposed 0m7.9s DEBUG: sources.list: deb http://mirror-ubc.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main deb http://mirror-ubc.debian.org/debian/ stretch-updates main deb http://mirror-ubc.debian.org/debian/ stretch-proposed-updates main 0m7.9s INFO: Running scripts pre_distupgrade 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'update'] 0m10.5s DUMP: Ign:1 http://mirror-ubc.debian.org/debian stretch InRelease Get:2 http://mirror-ubc.debian.org/debian stretch-updates InRelease [91.0 kB] Get:3 http://mirror-ubc.debian.org/debian stretch-proposed-updates InRelease [96.3 kB] Hit:4 http://mirror-ubc.debian.org/debian stretch Release Get:5 http://security.debian.org stretch/updates InRelease [94.3 kB] Get:6 http://mirror-ubc.debian.org/debian stretch-updates/main amd64 Packages [5148 B] Get:7 http://mirror-ubc.debian.org/debian stretch-updates/main Translation-en [4512 B] Get:8 http://mirror-ubc.debian.org/debian stretch-proposed-updates/main amd64 Packages [91.2 kB] Get:9 http://mirror-ubc.debian.org/debian stretch-proposed-updates/main Translation-en [56.6 kB] Get:11 http://security.debian.org stretch/updates/main amd64 Packages [447 kB] Get:12 http://security.debian.org stretch/updates/main Translation-en [192 kB] Fetched 1078 kB in 1s (950 kB/s) Reading package lists... 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'update'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-yf', 'dist-upgrade'] 0m10.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-yf', 'dist-upgrade'] 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m11.3s DUMP: f46be0fa513e485067cca09281ca0e37 - 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'show', '--no-all-versions', 'disulfinder'] 0m11.5s DUMP: Package: disulfinder Version: 1.2.11-6 Installed-Size: 726 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2), disulfinder-data Description-en: cysteines disulfide bonding state and connectivity predictor 'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. . 'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern. Description-md5: 5f70380c76687c70f279559ee87b7d0e Homepage: http://disulfind.dsi.unifi.it/ Tag: role::program Section: science Priority: extra Filename: pool/main/d/disulfinder/disulfinder_1.2.11-6_amd64.deb Size: 260686 MD5sum: 1e656f40725e9e28843c52dfc1334e4d SHA256: e047cb1432c30e46fe3e37b6ff7601489b4c8913ba6c3d4789fc6a0967599f6f 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'show', '--no-all-versions', 'disulfinder'] 0m11.5s INFO: apt-cache knows about the following packages: disulfinder 0m11.5s INFO: Running scripts pre_install 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m11.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian stretch-proposed-updates/main amd64 Packages release o=Debian,a=proposed-updates,n=stretch-proposed-updates,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org 500 http://mirror-ubc.debian.org/debian stretch-updates/main amd64 Packages release o=Debian,a=stable-updates,n=stretch-updates,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=stable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages release v=9.5,o=Debian,a=stable,n=stretch,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m11.7s DUMP: disulfinder: Installed: 1.2.11-6 Candidate: 1.2.11-6 Version table: *** 1.2.11-6 500 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder'] 0m12.1s DUMP: Reading package lists... Building dependency tree... Reading state information... disulfinder is already the newest version (1.2.11-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder'] 0m12.1s INFO: Running scripts post_install 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m12.1s INFO: Running scripts post_distupgrade 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m12.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m12.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m12.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m12.9s INFO: Running scripts pre_install 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m13.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror-ubc.debian.org/debian stretch-proposed-updates/main amd64 Packages release o=Debian,a=proposed-updates,n=stretch-proposed-updates,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org 500 http://mirror-ubc.debian.org/debian stretch-updates/main amd64 Packages release o=Debian,a=stable-updates,n=stretch-updates,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=stable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages release v=9.5,o=Debian,a=stable,n=stretch,l=Debian,c=main,b=amd64 origin mirror-ubc.debian.org Pinned packages: 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m13.2s DUMP: disulfinder: Installed: 1.2.11-6 Candidate: 1.2.11-6 Version table: *** 1.2.11-6 500 500 http://mirror-ubc.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-cache', 'policy', 'disulfinder'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder=1.2.11-6'] 0m13.8s DUMP: Reading package lists... Building dependency tree... Reading state information... disulfinder is already the newest version (1.2.11-6). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', '-y', 'install', 'disulfinder=1.2.11-6'] 0m13.8s INFO: Running scripts post_install 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m14.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.2s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.8 install ok installed base-files base-files 9.9+deb9u5 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 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed disulfinder disulfinder 1.2.11-6 install ok installed disulfinder-data disulfinder-data 1.2.11-6 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2 install ok installed e2fsprogs e2fsprogs 1.43.4-2 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~deb9u2 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 1.4.8 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+deb9u3 install ok installed libc6:amd64 libc6 2.24-11+deb9u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2 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 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u4 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u4 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+deb9u3 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+deb9u4 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 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', '-ac', '--ignore-obsolete'] 0m15.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', '-ac', '--ignore-obsolete'] 0m15.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.3s DUMP: 0.15.1 0m15.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m15.3s INFO: Running adequate version 0.15.1 now. 0m15.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'disulfinder'] 0m15.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'disulfinder'] 0m15.4s INFO: Running scripts pre_remove 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/pre_remove_exceptions'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'remove', 'disulfinder-data', 'disulfinder'] 0m17.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: disulfinder disulfinder-data 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. After this operation, 13.6 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 ... 4978 files and directories currently installed.) Removing disulfinder (1.2.11-6) ... Removing disulfinder-data (1.2.11-6) ... 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'remove', 'disulfinder-data', 'disulfinder'] 0m17.3s INFO: Running scripts post_remove 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_remove_exceptions'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_remove_exceptions'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', 'disulfinder-data'] 0m17.3s DUMP: dpkg: warning: ignoring request to remove disulfinder-data which isn't installed 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', 'disulfinder-data'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', 'disulfinder'] 0m17.3s DUMP: dpkg: warning: ignoring request to remove disulfinder which isn't installed 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', 'disulfinder'] 0m17.3s INFO: Running scripts post_purge 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_purge_exceptions'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_purge_exceptions'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', '--pending'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--purge', '--pending'] 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--remove', '--pending'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg', '--remove', '--pending'] 0m17.4s INFO: Running scripts post_test 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_test_exceptions'] 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'tmp/scripts/post_test_exceptions'] 0m17.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m18.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-divert', '--list'] 0m18.0s 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 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'dpkg-divert', '--list'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'clean'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpKYPcX_', 'apt-get', 'clean'] 0m18.0s DEBUG: Recording chroot state 0m19.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/shm'] 0m19.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/shm'] 0m19.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/console'] 0m19.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/console'] 0m19.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/ptmx'] 0m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/ptmx'] 0m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts'] 0m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/dev/pts'] 0m19.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/proc'] 0m19.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpKYPcX_/proc'] 0m19.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m19.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpKYPcX_'] 0m19.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpKYPcX_ 0m19.5s INFO: PASS: Upgrading between Debian distributions. 0m19.5s INFO: PASS: All tests. 0m19.5s INFO: piuparts run ends. ret=0 End: 2018-09-29 02:05:56 UTC