Start: 2023-03-22 20:08:16 GMT [wheezy] Package: bioperl-run Version: 1.6.9-1 Installed-Size: 144 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl (>= 1.6.0), libbio-perl-run-perl (= 1.6.9-1) Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons, samtools, sim4, t-coffee, tigr-glimmer, wise Suggests: gmap, paml, molphy, phylip, ensembl Description: BioPerl wrappers: scripts Homepage: http://www.bioperl.org/wiki/Run_package Description-md5: 7ae0a3a7ce278987fe66fde47a91ee2f Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program Section: science Priority: optional Filename: pool/main/b/bioperl-run/bioperl-run_1.6.9-1_all.deb Size: 46294 MD5sum: e4e1eab03f0dfd9ddebcac2b1e6aa767 SHA1: 30dd4a966b8be7143e4e550579bdb2db5eabca04 SHA256: 687f553a99475cdcdff833f3600c1899353541832cba9daf513f2b7fa2d0ce29 [jessie] Package: bioperl-run Version: 1.6.9-2 Installed-Size: 117 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, libbio-perl-run-perl (= 1.6.9-2) Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probalign, probcons, samtools, sim4, t-coffee, tigr-glimmer, wise Suggests: gmap, paml, phylip Description: BioPerl wrappers: scripts Homepage: http://www.bioperl.org/wiki/Run_package Description-md5: 7ae0a3a7ce278987fe66fde47a91ee2f Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program Section: science Priority: optional Filename: pool/main/b/bioperl-run/bioperl-run_1.6.9-2_all.deb Size: 44004 MD5sum: 904ba6a2dac1244e46a99cdeb37204a9 SHA1: 8af1e6a74e190b3decd296cef43d9ff20b1bc253 SHA256: 0ab6dfc37e2d3eb86c6f011b88f2514e2dd7d25598dfb219d6258fc997e49936 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-jessie --skip-logrotatefiles-test --warn-on-debsums-errors --warn-on-install-over-symlink -i /usr/lib/dbus-1.0/dbus-daemon-launch-helper --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d jessie -S /srv/piuparts.debian.org/slave/refchroot/wheezy2jessie-rcmd/reference-chroot-metadata.dat --apt bioperl-run=1.6.9-2 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 --install-recommends --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 -i /usr/lib/dbus-1.0/dbus-daemon-launch-helper --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy -d jessie -S /srv/piuparts.debian.org/slave/refchroot/wheezy2jessie-rcmd/reference-chroot-metadata.dat --apt bioperl-run=1.6.9-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpn27_wwk7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpn27_wwk7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/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/tmpn27_wwk7/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/run/shm'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/run/shm'] 0m1.4s DEBUG: sources.list: deb http://archive.debian.org/debian wheezy main 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Created resolv.conf. 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpn27_wwk7/tmp/scripts/ 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-jessie to /srv/piuparts.debian.org/tmp/tmpn27_wwk7/tmp/scripts/ 0m1.4s INFO: Running scripts post_chroot_unpack 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DUMP: Creating /etc/apt/apt.conf.d/unauthenticated-wheezy ... # The Release file is not getting updated. Acquire::Check-Valid-Until "false"; 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', 'apt-get', 'update'] 0m1.4s DUMP: E: Method http has died unexpectedly! E: Sub-process http received a segmentation fault. 0m1.4s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7', 'apt-get', 'update'] E: Method http has died unexpectedly! E: Sub-process http received a segmentation fault. 0m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/run/shm'] 0m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/run/shm'] 0m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/console'] 0m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/console'] 0m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/pts'] 0m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/dev/pts'] 0m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/proc'] 0m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7/proc'] 0m1.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7'] 0m1.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpn27_wwk7'] 0m1.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpn27_wwk7 0m1.9s ERROR: piuparts run ends. ret=1 End: 2023-03-22 20:08:18 GMT