Start: 2020-11-16 15:47:37 GMT [testing] Package: clustalw Version: 2.1+lgpl-6 Installed-Size: 775 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Description: global multiple nucleotide or peptide sequence alignment Homepage: http://www.clustal.org/clustal2/ Description-md5: 633246bd8fd1b951f15985f7cbfb1909 Tag: biology::format:aln, biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, interface::text-mode, role::program, scope::utility, use::comparing, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/c/clustalw/clustalw_2.1+lgpl-6_amd64.deb Size: 281852 MD5sum: 58836ece1b786b44a3cb2018f9ac5bfc SHA256: e9eca6c539a0e23d84d3da62446458cc83a5da18fa7907a91ab7c70d38b4fd83 [sid] Package: clustalw Version: 2.1+lgpl-7 Installed-Size: 787 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Description: global multiple nucleotide or peptide sequence alignment Homepage: http://www.clustal.org/clustal2/ Description-md5: 633246bd8fd1b951f15985f7cbfb1909 Tag: biology::format:aln, biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, interface::text-mode, role::program, scope::utility, use::comparing, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/c/clustalw/clustalw_2.1+lgpl-7_amd64.deb Size: 281716 MD5sum: 1f337e6420db5c739728ba80b42922d7 SHA256: 5b8bbe8ab8372b38b9a68c3468552fa81cf562c5e76892a922a180566824cdea 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt clustalw=2.1+lgpl-7 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 1.1.2~202004292056~1.1.1-20-gd7155993 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt clustalw=2.1+lgpl-7 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-12-amd64 #1 SMP Debian 4.19.152-1 (2020-10-18) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp4eeio6n7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp4eeio6n7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp4eeio6n7/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'update'] 0m5.2s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [7861 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6012 kB] Fetched 14.0 MB in 3s (4981 kB/s) Reading package lists... 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'update'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-yf', 'dist-upgrade'] 0m6.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: dash libidn2-0 libseccomp2 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 249 kB of archives. After this operation, 194 kB disk space will be freed. Get:1 http://deb.debian.org/debian bullseye/main amd64 dash amd64 0.5.11+git20200708+dd9ef66-2 [114 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libidn2-0 amd64 2.3.0-3 [86.0 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libseccomp2 amd64 2.5.0-3 [48.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 249 kB in 0s (6265 kB/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 ... 6650 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20200708+dd9ef66-2_amd64.deb ... Unpacking dash (0.5.11+git20200708+dd9ef66-2) over (0.5.10.2-7) ... Setting up dash (0.5.11+git20200708+dd9ef66-2) ... (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 ... 6650 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.0-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.0-3) over (2.3.0-2) ... Setting up libidn2-0:amd64 (2.3.0-3) ... (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 ... 6650 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.0-3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.0-3) over (2.4.4-1+b1) ... Setting up libseccomp2:amd64 (2.5.0-3) ... Processing triggers for libc-bin (2.31-4) ... 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-yf', 'dist-upgrade'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s DUMP: 585536727141623d0447b930f497a85b - 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.4s INFO: Running scripts post_setup 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_minimize'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_minimize'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_zz_backports'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_setup_zz_backports'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.9s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.11 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.48 install ok installed bash bash 5.1~rc2-1 install ok installed bsdutils bsdutils 1:2.36-3+b2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-2 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0+git20201010-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-16 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-18 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.4-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.58 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.11 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3.1 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3.1 install ok installed libblkid1:amd64 libblkid1 2.36-3+b2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-4 install ok installed libc6:amd64 libc6 2.31-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.17-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.255 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-4 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-16 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.0+dfsg-6 install ok installed libgnutls30:amd64 libgnutls30 3.6.15-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-10 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-10 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-10 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-10 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36-3+b2 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnss-nis:amd64 libnss-nis 3.1-4 install ok installed libnss-nisplus:amd64 libnss-nisplus 1.3-4 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.21-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.0-3 install ok installed libselinux1:amd64 libselinux1 3.1-2+b1 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36-3+b2 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1h-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 246.6-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20200918-1 install ok installed libtirpc-common libtirpc-common 1.2.6-3 install ok installed libtirpc3:amd64 libtirpc3 1.2.6-3 install ok installed libudev1:amd64 libudev1 246.6-2 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36-3+b2 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36-3+b2 install ok installed ncurses-base ncurses-base 6.2+20200918-1 install ok installed ncurses-bin ncurses-bin 6.2+20200918-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.30.3-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-5 install ok installed tar tar 1.30+dfsg-7 install ok installed tzdata tzdata 2020d-1 install ok installed util-linux util-linux 2.36-3+b2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m8.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m8.2s INFO: Running scripts is_testable 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/is_testable_uninstallable'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/is_testable_uninstallable'] 0m8.2s INFO: Running scripts pre_test 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_test_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_test_exceptions'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_test_root_password'] 0m8.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_test_root_password'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'show', '--no-all-versions', 'clustalw'] 0m8.5s DUMP: Package: clustalw Version: 2.1+lgpl-6 Installed-Size: 775 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Description-en: global multiple nucleotide or peptide sequence alignment This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal?W is very well accepted. . The output of Clustal?W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal?X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM. Description-md5: 633246bd8fd1b951f15985f7cbfb1909 Homepage: http://www.clustal.org/clustal2/ Tag: biology::format:aln, biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, interface::text-mode, role::program, scope::utility, use::comparing, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/c/clustalw/clustalw_2.1+lgpl-6_amd64.deb Size: 281852 MD5sum: 58836ece1b786b44a3cb2018f9ac5bfc SHA256: e9eca6c539a0e23d84d3da62446458cc83a5da18fa7907a91ab7c70d38b4fd83 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'show', '--no-all-versions', 'clustalw'] 0m8.5s INFO: apt-cache knows about the following packages: clustalw 0m8.5s INFO: Running scripts pre_install 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m8.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release o=Debian,a=testing,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m8.6s DUMP: clustalw: Installed: (none) Candidate: 2.1+lgpl-6 Version table: 2.1+lgpl-6 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw'] 0m9.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: clustalx seaview The following NEW packages will be installed: clustalw 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 282 kB of archives. After this operation, 794 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 clustalw amd64 2.1+lgpl-6 [282 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 282 kB in 0s (8609 kB/s) Selecting previously unselected package clustalw. (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 ... 6651 files and directories currently installed.) Preparing to unpack .../clustalw_2.1+lgpl-6_amd64.deb ... Unpacking clustalw (2.1+lgpl-6) ... Setting up clustalw (2.1+lgpl-6) ... 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw'] 0m9.2s INFO: Running scripts post_install 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m9.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m9.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m9.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp4eeio6n7 to sid 0m9.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.5s INFO: Running scripts pre_distupgrade 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'update'] 0m13.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [146 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8506 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6408 kB] Fetched 15.1 MB in 3s (5579 kB/s) Reading package lists... 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'update'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-yf', 'dist-upgrade'] 0m15.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils clustalw gcc-10-base grep libblkid1 libffi7 libgcc-s1 libgmp10 libmount1 libsmartcols1 libstdc++6 libuuid1 mount perl-base util-linux 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5741 kB of archives. After this operation, 2826 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.36-4 [148 kB] Get:2 http://deb.debian.org/debian sid/main amd64 grep amd64 3.6-1 [398 kB] Get:3 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.32.0-5 [1626 kB] Get:4 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.36-4 [1135 kB] Get:5 http://deb.debian.org/debian sid/main amd64 mount amd64 2.36-4 [184 kB] Get:6 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.2.0-17 [200 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 10.2.0-17 [492 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 10.2.0-17 [41.4 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.36-4 [195 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libffi7 amd64 3.3-5 [23.0 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.2.1+dfsg-1 [564 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.36-4 [212 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.36-4 [158 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.36-4 [82.6 kB] Get:15 http://deb.debian.org/debian sid/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5741 kB in 0s (49.1 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 ... 6668 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.36-4_amd64.deb ... Unpacking bsdutils (1:2.36-4) over (1:2.36-3+b2) ... Setting up bsdutils (1:2.36-4) ... (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 ... 6667 files and directories currently installed.) Preparing to unpack .../archives/grep_3.6-1_amd64.deb ... Unpacking grep (3.6-1) over (3.4-1) ... Setting up grep (3.6-1) ... (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 ... 6668 files and directories currently installed.) Preparing to unpack .../perl-base_5.32.0-5_amd64.deb ... Unpacking perl-base (5.32.0-5) over (5.30.3-4) ... Setting up perl-base (5.32.0-5) ... (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 ... 6698 files and directories currently installed.) Preparing to unpack .../util-linux_2.36-4_amd64.deb ... Unpacking util-linux (2.36-4) over (2.36-3+b2) ... Setting up util-linux (2.36-4) ... (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 ... 6697 files and directories currently installed.) Preparing to unpack .../mount_2.36-4_amd64.deb ... Unpacking mount (2.36-4) over (2.36-3+b2) ... Preparing to unpack .../gcc-10-base_10.2.0-17_amd64.deb ... Unpacking gcc-10-base:amd64 (10.2.0-17) over (10.2.0-16) ... Setting up gcc-10-base:amd64 (10.2.0-17) ... (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 ... 6696 files and directories currently installed.) Preparing to unpack .../libstdc++6_10.2.0-17_amd64.deb ... Unpacking libstdc++6:amd64 (10.2.0-17) over (10.2.0-16) ... Setting up libstdc++6:amd64 (10.2.0-17) ... (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 ... 6696 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10.2.0-17_amd64.deb ... Unpacking libgcc-s1:amd64 (10.2.0-17) over (10.2.0-16) ... Setting up libgcc-s1:amd64 (10.2.0-17) ... (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 ... 6696 files and directories currently installed.) Preparing to unpack .../libblkid1_2.36-4_amd64.deb ... Unpacking libblkid1:amd64 (2.36-4) over (2.36-3+b2) ... Setting up libblkid1:amd64 (2.36-4) ... (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 ... 6695 files and directories currently installed.) Preparing to unpack .../libffi7_3.3-5_amd64.deb ... Unpacking libffi7:amd64 (3.3-5) over (3.3-4) ... Setting up libffi7:amd64 (3.3-5) ... (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 ... 6695 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.1+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.1+dfsg-1) over (2:6.2.0+dfsg-6) ... Setting up libgmp10:amd64 (2:6.2.1+dfsg-1) ... (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 ... 6696 files and directories currently installed.) Preparing to unpack .../libmount1_2.36-4_amd64.deb ... Unpacking libmount1:amd64 (2.36-4) over (2.36-3+b2) ... Setting up libmount1:amd64 (2.36-4) ... (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 ... 6695 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.36-4_amd64.deb ... Unpacking libsmartcols1:amd64 (2.36-4) over (2.36-3+b2) ... Setting up libsmartcols1:amd64 (2.36-4) ... (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 ... 6694 files and directories currently installed.) Preparing to unpack .../libuuid1_2.36-4_amd64.deb ... Unpacking libuuid1:amd64 (2.36-4) over (2.36-3+b2) ... Setting up libuuid1:amd64 (2.36-4) ... (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 ... 6693 files and directories currently installed.) Preparing to unpack .../clustalw_2.1+lgpl-7_amd64.deb ... Unpacking clustalw (2.1+lgpl-7) over (2.1+lgpl-6) ... Setting up mount (2.36-4) ... Setting up clustalw (2.1+lgpl-7) ... Processing triggers for libc-bin (2.31-4) ... 0m15.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-yf', 'dist-upgrade'] 0m15.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.4s DUMP: 12a3c53496ab3ff517ce3e62a9f948a3 - 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'show', '--no-all-versions', 'clustalw'] 0m15.6s DUMP: Package: clustalw Version: 2.1+lgpl-7 Installed-Size: 787 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2) Suggests: clustalx, seaview Enhances: bioperl-run, emboss, t-coffee Description-en: global multiple nucleotide or peptide sequence alignment This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal?W is very well accepted. . The output of Clustal?W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal?X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM. Description-md5: 633246bd8fd1b951f15985f7cbfb1909 Homepage: http://www.clustal.org/clustal2/ Tag: biology::format:aln, biology::peptidic, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, interface::text-mode, role::program, scope::utility, use::comparing, works-with-format::plaintext, works-with::TODO Section: science Priority: optional Filename: pool/main/c/clustalw/clustalw_2.1+lgpl-7_amd64.deb Size: 281716 MD5sum: 1f337e6420db5c739728ba80b42922d7 SHA256: 5b8bbe8ab8372b38b9a68c3468552fa81cf562c5e76892a922a180566824cdea 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'show', '--no-all-versions', 'clustalw'] 0m15.6s INFO: apt-cache knows about the following packages: clustalw 0m15.6s INFO: Running scripts pre_install 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m15.7s 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: 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m15.7s DUMP: clustalw: Installed: 2.1+lgpl-7 Candidate: 2.1+lgpl-7 Version table: *** 2.1+lgpl-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw'] 0m16.0s DUMP: Reading package lists... Building dependency tree... Reading state information... clustalw is already the newest version (2.1+lgpl-7). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw'] 0m16.0s INFO: Running scripts post_install 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m16.0s INFO: Running scripts post_distupgrade 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m16.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m16.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m16.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m16.5s INFO: Running scripts pre_install 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_database-server'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_exceptions'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_extras'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m16.6s 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: 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m16.6s DUMP: clustalw: Installed: 2.1+lgpl-7 Candidate: 2.1+lgpl-7 Version table: *** 2.1+lgpl-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-cache', 'policy', 'clustalw'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw=2.1+lgpl-7'] 0m17.0s DUMP: Reading package lists... Building dependency tree... Reading state information... clustalw is already the newest version (2.1+lgpl-7). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', '-y', 'install', 'clustalw=2.1+lgpl-7'] 0m17.0s INFO: Running scripts post_install 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_install_exceptions'] 0m17.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m17.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m17.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', '-ac', '--ignore-obsolete'] 0m18.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', '-ac', '--ignore-obsolete'] 0m18.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.3s DUMP: 0.15.2 0m18.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.3s INFO: Running adequate version 0.15.2 now. 0m18.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'clustalw'] 0m18.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'clustalw'] 0m18.4s INFO: Running scripts pre_remove 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_exceptions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/pre_remove_exceptions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.11 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.48 install ok installed bash bash 5.1~rc2-1 install ok installed bsdutils bsdutils 1:2.36-4 install ok installed clustalw clustalw 2.1+lgpl-7 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-2 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0+git20201010-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-17 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-18 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.58 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.11 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3.1 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3.1 install ok installed libblkid1:amd64 libblkid1 2.36-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-4 install ok installed libc6:amd64 libc6 2.31-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.17-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.255 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-5 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-17 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.6.15-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-10 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-10 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-10 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-10 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36-4 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnss-nis:amd64 libnss-nis 3.1-4 install ok installed libnss-nisplus:amd64 libnss-nisplus 1.3-4 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.21-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.0-3 install ok installed libselinux1:amd64 libselinux1 3.1-2+b1 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36-4 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1h-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-17 install ok installed libsystemd0:amd64 libsystemd0 246.6-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20200918-1 install ok installed libtirpc-common libtirpc-common 1.2.6-3 install ok installed libtirpc3:amd64 libtirpc3 1.2.6-3 install ok installed libudev1:amd64 libudev1 246.6-2 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36-4 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36-4 install ok installed ncurses-base ncurses-base 6.2+20200918-1 install ok installed ncurses-bin ncurses-bin 6.2+20200918-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.0-5 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-5 install ok installed tar tar 1.30+dfsg-7 install ok installed tzdata tzdata 2020d-1 install ok installed util-linux util-linux 2.36-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'remove', 'clustalw'] 0m19.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: clustalw 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 806 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 ... 6693 files and directories currently installed.) Removing clustalw (2.1+lgpl-7) ... 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'remove', 'clustalw'] 0m19.8s INFO: Running scripts post_remove 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_remove_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_remove_exceptions'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--purge', 'clustalw'] 0m19.9s DUMP: (Reading database ... 6676 files and directories currently installed.) Purging configuration files for clustalw (2.1+lgpl-7) ... 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--purge', 'clustalw'] 0m19.9s INFO: Running scripts post_purge 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_purge_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_purge_exceptions'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--purge', '--pending'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--purge', '--pending'] 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--remove', '--pending'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg', '--remove', '--pending'] 0m19.9s INFO: Running scripts post_test 0m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_test_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'tmp/scripts/post_test_exceptions'] 0m19.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m20.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-divert', '--list'] 0m20.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'dpkg-divert', '--list'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'clean'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7', 'apt-get', 'clean'] 0m20.2s DEBUG: Recording chroot state 0m20.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/shm'] 0m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/shm'] 0m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/console'] 0m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/console'] 0m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/ptmx'] 0m20.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/ptmx'] 0m20.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts'] 0m21.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/dev/pts'] 0m21.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/proc'] 0m21.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7/proc'] 0m21.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m21.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp4eeio6n7'] 0m21.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp4eeio6n7 0m21.1s INFO: PASS: Upgrading between Debian distributions. 0m21.1s INFO: PASS: All tests. 0m21.1s INFO: piuparts run ends. ret=0 End: 2020-11-16 15:47:58 GMT