Start: 2023-02-22 16:21:48 GMT [jessie-lts] Package: clonalframe Version: 1.2-3 Installed-Size: 143 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libgsl0ldbl (>= 1.9), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0) Description: inference of bacterial microevolution using multilocus sequence data Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Description-md5: 50761e6f91c58a640bf4e38995728ecd Tag: implemented-in::c++, role::program Section: science Priority: optional Filename: pool/main/c/clonalframe/clonalframe_1.2-3_amd64.deb Size: 54960 MD5sum: d2fee6e3f43cf82eaddb029a9ea3e4e0 SHA1: 15467ceaaa7c6d92cc1dcf585db71801b49c1d6c SHA256: 0af8cf1558e19af5cc0114f97762b08c8e1e943dde0e7c0ca23db81bec7e2f81 [stretch] Package: clonalframe Version: 1.2-5 Installed-Size: 121 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgsl2, libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 5.2) Description: inference of bacterial microevolution using multilocus sequence data Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Description-md5: 819b92534a0771df03d25aa1b0334115 Tag: implemented-in::c++, role::program Section: science Priority: optional Filename: pool/main/c/clonalframe/clonalframe_1.2-5_amd64.deb Size: 49222 MD5sum: 20cbb58ada3a9fec04c6e8a1df2c6420 SHA256: 7da16292d6b350cce26b98a9c31fb07a0aebd4aff9dfcd8d5cde16150a34172b 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 clonalframe=1.2-5 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 clonalframe=1.2-5 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/tmponb69f53 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmponb69f53 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmponb69f53', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmponb69f53', '-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/tmponb69f53/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmponb69f53/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/tmponb69f53/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/tmponb69f53/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main deb http://security.debian.org jessie/updates main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmponb69f53/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', 'update'] 0m3.1s DUMP: Get:1 http://security.debian.org jessie/updates InRelease [44.9 kB] Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Get:2 http://security.debian.org jessie/updates/main amd64 Packages [781 kB] Ign http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main Translation-en Hit http://deb.debian.org jessie/main amd64 Packages Get:3 http://security.debian.org jessie/updates/main Translation-en [401 kB] Fetched 1227 kB in 0s (1666 kB/s) Reading package lists... W: GPG error: http://deb.debian.org jessie Release: The following signatures were invalid: KEYEXPIRED 1668891673 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', 'update'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s 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 (38.2 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 ... 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 ... 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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 ... 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 Feb 22 16:21:55 UTC 2023. Universal Time is now: Wed Feb 22 16:21:55 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s DUMP: ea587cb5da6f95fbc79bf1681671e909 - 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.9s INFO: Running scripts post_setup 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_dummy_users'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_dummy_users'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_forbid_home'] 0m7.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_forbid_home'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_minimize'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_minimize'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_zz_backports'] 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/post_setup_zz_backports'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.7s 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 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie-lts2stretch/reference-chroot-metadata.dat 0m7.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmponb69f53'] 0m8.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmponb69f53'] 0m8.1s INFO: Running scripts is_testable 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/is_testable_uninstallable'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/is_testable_uninstallable'] 0m8.1s INFO: Running scripts pre_test 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_test_exceptions'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_test_exceptions'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_test_root_password'] 0m8.1s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_test_root_password'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'show', '--no-all-versions', 'clonalframe'] 0m8.2s DUMP: Package: clonalframe Version: 1.2-3 Installed-Size: 143 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libgsl0ldbl (>= 1.9), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.4.0) Description-en: inference of bacterial microevolution using multilocus sequence data ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. . ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame. Description-md5: 50761e6f91c58a640bf4e38995728ecd Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Tag: implemented-in::c++, role::program Section: science Priority: optional Filename: pool/main/c/clonalframe/clonalframe_1.2-3_amd64.deb Size: 54960 MD5sum: d2fee6e3f43cf82eaddb029a9ea3e4e0 SHA1: 15467ceaaa7c6d92cc1dcf585db71801b49c1d6c SHA256: 0af8cf1558e19af5cc0114f97762b08c8e1e943dde0e7c0ca23db81bec7e2f81 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'show', '--no-all-versions', 'clonalframe'] 0m8.2s INFO: apt-cache knows about the following packages: clonalframe 0m8.2s INFO: Running scripts pre_install 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_database-server'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_database-server'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_exceptions'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_extras'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_extras'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'policy'] 0m8.2s 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: 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'policy'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'policy', 'clonalframe'] 0m8.2s DUMP: clonalframe: Installed: (none) Candidate: 1.2-3 Version table: 1.2-3 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-cache', 'policy', 'clonalframe'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', '-y', 'install', 'clonalframe'] 0m8.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: fontconfig fontconfig-config fonts-dejavu-core libaudio2 libbsd0 libexpat1 libffi6 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0ldbl libice6 libjbig0 libjpeg62-turbo liblcms2-2 libmng1 libpng12-0 libqtcore4 libqtgui4 libsm6 libtiff5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxrender1 libxt6 qtcore4-l10n ucf x11-common Suggested packages: nas gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html liblcms2-utils libicu52 libthai0 qt4-qtconfig Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs libcups2 The following NEW packages will be installed: clonalframe fontconfig fontconfig-config fonts-dejavu-core libaudio2 libbsd0 libexpat1 libffi6 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0ldbl libice6 libjbig0 libjpeg62-turbo liblcms2-2 libmng1 libpng12-0 libqtcore4 libqtgui4 libsm6 libtiff5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxrender1 libxt6 qtcore4-l10n ucf x11-common 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 15.1 MB of archives. After this operation, 44.2 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpng12-0 ucf fonts-dejavu-core libxau6 x11-common libsm6 libxcb1 libxt6 libaudio2 libmng1 libjbig0 libxext6 libxrender1 libgsl0ldbl clonalframe E: There are problems and -y was used without --force-yes 0m8.5s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmponb69f53', 'apt-get', '-y', 'install', 'clonalframe'] Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: fontconfig fontconfig-config fonts-dejavu-core libaudio2 libbsd0 libexpat1 libffi6 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0ldbl libice6 libjbig0 libjpeg62-turbo liblcms2-2 libmng1 libpng12-0 libqtcore4 libqtgui4 libsm6 libtiff5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxrender1 libxt6 qtcore4-l10n ucf x11-common Suggested packages: nas gsl-ref-psdoc gsl-doc-pdf gsl-doc-info gsl-ref-html liblcms2-utils libicu52 libthai0 qt4-qtconfig Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs libcups2 The following NEW packages will be installed: clonalframe fontconfig fontconfig-config fonts-dejavu-core libaudio2 libbsd0 libexpat1 libffi6 libfontconfig1 libfreetype6 libglib2.0-0 libgsl0ldbl libice6 libjbig0 libjpeg62-turbo liblcms2-2 libmng1 libpng12-0 libqtcore4 libqtgui4 libsm6 libtiff5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxrender1 libxt6 qtcore4-l10n ucf x11-common 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 15.1 MB of archives. After this operation, 44.2 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpng12-0 ucf fonts-dejavu-core libxau6 x11-common libsm6 libxcb1 libxt6 libaudio2 libmng1 libjbig0 libxext6 libxrender1 libgsl0ldbl clonalframe E: There are problems and -y was used without --force-yes 0m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/shm'] 0m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/shm'] 0m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/console'] 0m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/console'] 0m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/ptmx'] 0m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/ptmx'] 0m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/pts'] 0m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/dev/pts'] 0m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/proc'] 0m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmponb69f53/proc'] 0m8.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmponb69f53'] 0m8.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmponb69f53'] 0m8.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmponb69f53 0m8.9s ERROR: piuparts run ends. ret=1 End: 2023-02-22 16:21:57 GMT