Start: 2024-04-14 10:31:13 GMT Package: t-coffee Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Installed-Size: 2715 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Description: Multiple Sequence Alignment Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Description-md5: d9e3464438ee56699a59a136061af5df Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::analysing, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/t/t-coffee/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb Size: 1031640 MD5sum: e45c14907e44405908ce7186b67df396 SHA256: a9f4c84d7548b40576cd2cc07d1b0ac7990184728965fd33d7dac2014730f514 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-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 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 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt t-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpg5_2pesl 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpg5_2pesl 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpg5_2pesl/tmp/scripts/ 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpg5_2pesl/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'update'] 0m5.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9899 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7190 kB] Fetched 17.3 MB in 3s (4995 kB/s) Reading package lists... 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'update'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libdb5.3t64 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 697 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 697 kB in 0s (15.1 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 ... 5200 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) over (5.3.28+dfsg2-6) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Processing triggers for libc-bin (2.37-17) ... 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s DUMP: 1dd3d8f260d756536c7ed69a1709c801 - 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s INFO: Running scripts post_setup 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_fake-essential'] 0m9.7s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Reading state information... init-system-helpers is already the newest version (1.66). The following additional packages will be installed: sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks The following NEW packages will be installed: dbconfig-common sensible-utils ucf 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 670 kB of archives. After this operation, 1826 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:3 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 670 kB in 0s (15.0 MB/s) Selecting previously unselected package sensible-utils. (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 ... 5200 files and directories currently installed.) Preparing to unpack .../sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package ucf. Preparing to unpack .../ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../dbconfig-common_2.0.24_all.deb ... Unpacking dbconfig-common (2.0.24) ... Setting up sensible-utils (0.0.22) ... Setting up ucf (3.0043+nmu1) ... Setting up dbconfig-common (2.0.24) ... Creating config file /etc/dbconfig-common/config with new version 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_fake-essential'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_forbid_home'] 0m9.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_forbid_home'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_minimize'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_minimize'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_zz_backports'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_setup_zz_backports'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m9.7s DEBUG: Recording chroot state 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.4s DUMP: install ok installed apt apt 2.9.0 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-17 install ok installed libc6:amd64 libc6 2.37-17 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-5 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed ucf ucf 3.0043+nmu1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-divert', '--list'] 0m10.4s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-divert', '--list'] 0m10.4s INFO: Running scripts is_testable 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/is_testable_uninstallable'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/is_testable_uninstallable'] 0m10.4s INFO: apt-cache does not know about any of the requested packages 0m10.4s INFO: Running scripts pre_test 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_test_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_test_exceptions'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_test_root_password'] 0m10.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_test_root_password'] 0m10.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m11.7s DEBUG: No broken symlinks as far as we can find. 0m11.7s INFO: Running scripts pre_install 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'show', '--no-all-versions', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m13.1s DUMP: Package: t-coffee Version: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Installed-Size: 2715 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Recommends: amap-align, clustalo, clustalw, dialign-tx, fsa, kalign, libsoap-lite-perl, libxml-simple-perl, mafft, muscle, mustang, ncbi-blast+, poa, prank, probcons, proda, tm-align Suggests: boxshade, seaview, t-coffee-examples Description-en: Multiple Sequence Alignment T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. . T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information . T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal?W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal?W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. Description-md5: d9e3464438ee56699a59a136061af5df Homepage: https://www.tcoffee.org/Projects/tcoffee/index.html Tag: field::biology, field::biology:bioinformatics, implemented-in::c, interface::commandline, role::program, scope::utility, use::analysing, use::comparing, works-with-format::TODO, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/t/t-coffee/t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb Size: 1031640 MD5sum: e45c14907e44405908ce7186b67df396 SHA256: a9f4c84d7548b40576cd2cc07d1b0ac7990184728965fd33d7dac2014730f514 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'show', '--no-all-versions', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m13.1s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: piuparts developers team Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 4.1.1) Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m13.1s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpp7hs_nzu/piuparts-depends-dummy'] 0m13.1s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpp7hs_nzu/piuparts-depends-dummy.deb'. 0m13.1s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpp7hs_nzu/piuparts-depends-dummy'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m13.1s DUMP: 2.9.0 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m13.1s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpp7hs_nzu/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpg5_2pesl/tmp 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m14.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: piuparts-depends-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/668 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy amd64 0.invalid.0 [668 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package piuparts-depends-dummy. (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 ... 5552 files and directories currently installed.) Preparing to unpack .../tmp/piuparts-depends-dummy.deb ... Unpacking piuparts-depends-dummy (0.invalid.0) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m14.1s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m14.1s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpg5_2pesl/./tmp/piuparts-depends-dummy.deb 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m14.1s DUMP: piuparts-depends-dummy install ok installed 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m14.1s DUMP: (Reading database ... 5552 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m14.2s DEBUG: Recording chroot state 0m14.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m15.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m16.0s DEBUG: No broken symlinks as far as we can find. 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m17.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m17.2s DUMP: t-coffee: Installed: (none) Candidate: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Version table: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m18.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: boxshade seaview t-coffee-examples Recommended packages: amap-align clustalo clustalw dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl mafft muscle mustang ncbi-blast+ poa prank probcons proda tm-align The following NEW packages will be installed: t-coffee 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1032 kB of archives. After this operation, 2780 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1032 kB in 0s (21.5 MB/s) Selecting previously unselected package t-coffee. (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 ... 5552 files and directories currently installed.) Preparing to unpack .../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m18.2s INFO: Running scripts post_install 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'remove', 't-coffee'] 0m19.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: t-coffee 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 2780 kB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5560 files and directories currently installed.) Removing t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'remove', 't-coffee'] 0m19.2s INFO: Reinstalling after remove 0m19.2s INFO: Running scripts pre_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m19.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m19.4s DUMP: t-coffee: Installed: (none) Candidate: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Version table: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m20.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: boxshade seaview t-coffee-examples Recommended packages: amap-align clustalo clustalw dialign-tx fsa kalign libsoap-lite-perl libxml-simple-perl mafft muscle mustang ncbi-blast+ poa prank probcons proda tm-align The following NEW packages will be installed: t-coffee debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/1032 kB of archives. After this operation, 2780 kB of additional disk space will be used. Selecting previously unselected package t-coffee. (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 ... 5552 files and directories currently installed.) Preparing to unpack .../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m20.6s INFO: Running scripts post_install 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m20.6s INFO: Running scripts pre_install 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_exceptions'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_extras'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m20.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m20.7s DUMP: t-coffee: Installed: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Candidate: 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 Version table: *** 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-cache', 'policy', 't-coffee'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', '--reinstall', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m21.9s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/1032 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 5560 files and directories currently installed.) Preparing to unpack .../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) over (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', '-y', 'install', '--reinstall', 't-coffee=13.45.0.4846264+really13.41.0.28bdc39+dfsg-1'] 0m21.9s INFO: Running scripts post_install 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m22.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m23.2s DEBUG: No broken symlinks as far as we can find. 0m23.2s INFO: /bin converted to /usr/bin by /usr merge 0m23.2s INFO: /lib converted to /usr/lib by /usr merge 0m23.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m23.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m23.2s INFO: /sbin converted to /usr/sbin by /usr merge 0m23.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', '-ac', '--ignore-obsolete'] 0m24.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', '-ac', '--ignore-obsolete'] 0m24.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.6s DUMP: 0.15.6 0m24.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.6s INFO: Running adequate version 0.15.6 now. 0m24.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 't-coffee'] 0m24.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 't-coffee'] 0m24.8s INFO: Running scripts pre_remove 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_exceptions'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_exceptions'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.6s DUMP: install ok installed apt apt 2.9.0 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-17 install ok installed libc6:amd64 libc6 2.37-17 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-5 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed t-coffee t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed ucf ucf 3.0043+nmu1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'remove', 't-coffee'] 0m26.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: t-coffee 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 2780 kB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5560 files and directories currently installed.) Removing t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'remove', 't-coffee'] 0m26.5s INFO: Running scripts post_remove 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_remove_cleanup'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_remove_cleanup'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_remove_exceptions'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_remove_exceptions'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', 't-coffee'] 0m26.6s DUMP: dpkg: warning: ignoring request to remove t-coffee which isn't installed 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', 't-coffee'] 0m26.6s INFO: Running scripts post_purge 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_purge_exceptions'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_purge_exceptions'] 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_purge_manual_cleanup'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_purge_manual_cleanup'] 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', '--pending'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--purge', '--pending'] 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--remove', '--pending'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg', '--remove', '--pending'] 0m26.6s INFO: Running scripts post_test 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_test_exceptions'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'tmp/scripts/post_test_exceptions'] 0m26.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m27.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m27.9s DEBUG: No broken symlinks as far as we can find. 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-divert', '--list'] 0m27.9s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'dpkg-divert', '--list'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl', 'apt-get', 'clean'] 0m27.9s DEBUG: Recording chroot state 0m28.8s INFO: PASS: Installation and purging test. 0m29.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/shm'] 0m29.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/shm'] 0m29.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/console'] 0m29.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/console'] 0m29.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/ptmx'] 0m29.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/ptmx'] 0m29.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts'] 0m29.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/dev/pts'] 0m29.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/proc'] 0m29.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl/proc'] 0m29.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m29.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpg5_2pesl'] 0m29.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpg5_2pesl 0m29.4s INFO: PASS: All tests. 0m29.4s INFO: piuparts run ends. ret=0 End: 2024-04-14 10:31:43 GMT