Start: 2023-03-15 14:04:44 GMT [jessie-lts] Package: probalign Version: 1.4-3 Installed-Size: 202 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Description: multiple sequence alignment using partition function posterior probabilities Homepage: http://cs.njit.edu/usman/probalign/ Description-md5: 3a11d1cc47a7d13a0473a4a4d2ff5aca Section: science Priority: optional Filename: pool/main/p/probalign/probalign_1.4-3_amd64.deb Size: 67900 MD5sum: a72317259c27be0a5015e3ae5ac2abdd SHA1: 757006831dcc715df9043b2b32238afd68592ba1 SHA256: 89acb9c298bc6121e045bd40cfd8dcde64c7cca08948e46806cb8204daf04684 [stretch] Package: probalign Version: 1.4-5 Installed-Size: 164 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2) Description: multiple sequence alignment using partition function posterior probabilities Homepage: http://probalign.njit.edu/standalone.html Description-md5: 3a11d1cc47a7d13a0473a4a4d2ff5aca Section: science Priority: optional Filename: pool/main/p/probalign/probalign_1.4-5_amd64.deb Size: 65438 MD5sum: ef5a674c2b02f90f2cc495b40f705034 SHA256: 8028dfa6fe826b371071c0ad5a2e21c01e1d43169010d23c7d760a103fe7561b 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 --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie-lts -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie-lts2stretch/reference-chroot-metadata.dat --apt probalign=1.4-5 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 --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie-lts -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie-lts2stretch/reference-chroot-metadata.dat --apt probalign=1.4-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfhb89kvs 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfhb89kvs 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main deb http://security.debian.org jessie/updates main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfhb89kvs/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', 'update'] 0m3.2s DUMP: Get:1 http://security.debian.org jessie/updates InRelease [44.9 kB] Ign http://deb.debian.org jessie InRelease Get:2 http://security.debian.org jessie/updates/main amd64 Packages [781 kB] Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Ign http://deb.debian.org jessie Release Get:3 http://security.debian.org jessie/updates/main Translation-en [401 kB] Hit http://deb.debian.org jessie/main Translation-en Hit http://deb.debian.org jessie/main amd64 Packages Fetched 1227 kB in 0s (1559 kB/s) Reading package lists... W: GPG error: http://deb.debian.org jessie Release: The following signatures were invalid: KEYEXPIRED 1668891673 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', 'update'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', '-yf', 'dist-upgrade'] 0m6.8s DUMP: Reading package lists... Building dependency tree... The following packages will be upgraded: apt bash e2fslibs e2fsprogs gcc-4.9-base libapt-pkg4.12 libbz2-1.0 libcomerr2 libgcc1 libgcrypt20 libss2 libstdc++6 libsystemd0 libudev1 perl-base systemd systemd-sysv tar tzdata udev zlib1g 21 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 gcc-4.9-base amd64 4.9.2-10+deb8u2 [160 kB] Get:8 http://security.debian.org/ jessie/updates/main libgcc1 amd64 1:4.9.2-10+deb8u2 [39.4 kB] Get:9 http://security.debian.org/ jessie/updates/main libstdc++6 amd64 4.9.2-10+deb8u2 [273 kB] Get:10 http://security.debian.org/ jessie/updates/main zlib1g amd64 1:1.2.8.dfsg-2+deb8u1 [88.3 kB] Get:11 http://security.debian.org/ jessie/updates/main libapt-pkg4.12 amd64 1.0.9.8.6 [794 kB] Get:12 http://security.debian.org/ jessie/updates/main apt amd64 1.0.9.8.6 [1109 kB] Get:13 http://security.debian.org/ jessie/updates/main libudev1 amd64 215-17+deb8u13 [58.8 kB] Get:14 http://security.debian.org/ jessie/updates/main udev amd64 215-17+deb8u13 [878 kB] Get:15 http://security.debian.org/ jessie/updates/main libcomerr2 amd64 1.42.12-2+deb8u2 [60.6 kB] Get:16 http://security.debian.org/ jessie/updates/main libss2 amd64 1.42.12-2+deb8u2 [64.9 kB] Get:17 http://security.debian.org/ jessie/updates/main libgcrypt20 amd64 1.6.3-2+deb8u8 [394 kB] Get:18 http://security.debian.org/ jessie/updates/main libsystemd0 amd64 215-17+deb8u13 [90.5 kB] Get:19 http://security.debian.org/ jessie/updates/main systemd amd64 215-17+deb8u13 [2555 kB] Get:20 http://security.debian.org/ jessie/updates/main systemd-sysv amd64 215-17+deb8u13 [37.5 kB] Get:21 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 (39.2 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 ... 7447 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 ... 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(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 ... 7445 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 ... 7445 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 ... 7444 files and directories currently installed.) 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 ... 7444 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 ... 7444 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 ... 7444 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 ... 7443 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 ... 7443 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 ... 7443 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 ... 7443 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 ... 7443 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 ... 7442 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 ... 7441 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 ... 7441 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 ... 7441 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 ... 7441 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 ... 7441 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: Wed Mar 15 14:04:51 UTC 2023. Universal Time is now: Wed Mar 15 14:04:51 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', '-yf', 'dist-upgrade'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s DUMP: ea587cb5da6f95fbc79bf1681671e909 - 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s INFO: Running scripts post_setup 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s 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 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 libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u2 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u8 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+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 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 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 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie-lts2stretch/reference-chroot-metadata.dat 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs'] 0m8.9s INFO: Running scripts is_testable 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s INFO: Running scripts pre_test 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_test_root_password'] 0m9.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_test_root_password'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'show', '--no-all-versions', 'probalign'] 0m9.0s DUMP: Package: probalign Version: 1.4-3 Installed-Size: 202 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Description-en: multiple sequence alignment using partition function posterior probabilities Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading alignment programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequences. On heteregeneous length datasets containing repeats Probalign alignment accuracy is 10% and 15% higher than the other three methods when standard deviation of length is at least 300 and 400. Description-md5: 3a11d1cc47a7d13a0473a4a4d2ff5aca Homepage: http://cs.njit.edu/usman/probalign/ Section: science Priority: optional Filename: pool/main/p/probalign/probalign_1.4-3_amd64.deb Size: 67900 MD5sum: a72317259c27be0a5015e3ae5ac2abdd SHA1: 757006831dcc715df9043b2b32238afd68592ba1 SHA256: 89acb9c298bc6121e045bd40cfd8dcde64c7cca08948e46806cb8204daf04684 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'show', '--no-all-versions', 'probalign'] 0m9.0s INFO: apt-cache knows about the following packages: probalign 0m9.0s INFO: Running scripts pre_install 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_database-server'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_database-server'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_exceptions'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_extras'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_extras'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'policy'] 0m9.0s 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: 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'policy'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'policy', 'probalign'] 0m9.1s DUMP: probalign: Installed: (none) Candidate: 1.4-3 Version table: 1.4-3 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-cache', 'policy', 'probalign'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', '-y', 'install', 'probalign'] 0m9.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: probalign 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 67.9 kB of archives. After this operation, 207 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! probalign E: There are problems and -y was used without --force-yes 0m9.3s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs', 'apt-get', '-y', 'install', 'probalign'] Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: probalign 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 67.9 kB of archives. After this operation, 207 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! probalign E: There are problems and -y was used without --force-yes 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/shm'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/shm'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/console'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/console'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/ptmx'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/ptmx'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/dev/pts'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/proc'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs/proc'] 0m9.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs'] 0m9.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfhb89kvs'] 0m9.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfhb89kvs 0m9.9s ERROR: piuparts run ends. ret=1 End: 2023-03-15 14:04:54 GMT