Start: 2020-11-15 20:50:46 GMT [testing] Package: fsa Version: 1.15.9+dfsg-5 Installed-Size: 4254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), mummer, exonerate Recommends: med-config (>= 2.1) Description: Fast Statistical Alignment of protein, RNA or DNA sequences Homepage: http://fsa.sourceforge.net/ Description-md5: 6250169bc99ea71aef4983021689c512 Section: science Priority: optional Filename: pool/main/f/fsa/fsa_1.15.9+dfsg-5_amd64.deb Size: 700000 MD5sum: 2b9959b771dd41b3007fd37a88988089 SHA256: bc1f2c3cf46fb282219e863ee15a9a769e860b0a3141b44a41e147dc0121d252 [sid] Package: fsa Version: 1.15.9+dfsg-6 Installed-Size: 4254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), mummer, exonerate Recommends: med-config (>= 2.1) Description: Fast Statistical Alignment of protein, RNA or DNA sequences Homepage: http://fsa.sourceforge.net/ Description-md5: 6250169bc99ea71aef4983021689c512 Section: science Priority: optional Filename: pool/main/f/fsa/fsa_1.15.9+dfsg-6_amd64.deb Size: 699936 MD5sum: 3a5a89e181ad156b3a5b981f38c9b0f0 SHA256: fe5b2aa4210ef3a1e676108a160416106354054310d47c01d8262fefb6255bb3 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 fsa=1.15.9+dfsg-6 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 1.1.2~202004292038~1.1.1-19-g418151e2 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 fsa=1.15.9+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmpmejp_h84 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmejp_h84 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/shm'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/shm'] 0m1.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpmejp_h84/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [7859 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6013 kB] Fetched 14.0 MB in 2s (6024 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-yf', 'dist-upgrade'] 0m5.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: dash libseccomp2 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 163 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 libseccomp2 amd64 2.5.0-3 [48.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 163 kB in 0s (1993 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 .../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) ... 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-yf', 'dist-upgrade'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.3s DUMP: 38047ab4e372d9573f127878f7065b57 - 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.3s INFO: Running scripts post_setup 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_dummy_users'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_dummy_users'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_forbid_home'] 0m6.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_forbid_home'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.3s 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' 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_minimize'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_minimize'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_zz_backports'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_setup_zz_backports'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s 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 2.3.0-2 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 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m6.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m6.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m6.9s INFO: Running scripts is_testable 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/is_testable_uninstallable'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/is_testable_uninstallable'] 0m6.9s INFO: Running scripts pre_test 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_test_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_test_exceptions'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_test_root_password'] 0m6.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_test_root_password'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'show', '--no-all-versions', 'fsa'] 0m7.1s DUMP: Package: fsa Version: 1.15.9+dfsg-5 Installed-Size: 4254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), mummer, exonerate Recommends: med-config (>= 2.1) Description-en: Fast Statistical Alignment of protein, RNA or DNA sequences FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz. . FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments: * FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints. * FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy. * FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above. * The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned Description-md5: 6250169bc99ea71aef4983021689c512 Homepage: http://fsa.sourceforge.net/ Section: science Priority: optional Filename: pool/main/f/fsa/fsa_1.15.9+dfsg-5_amd64.deb Size: 700000 MD5sum: 2b9959b771dd41b3007fd37a88988089 SHA256: bc1f2c3cf46fb282219e863ee15a9a769e860b0a3141b44a41e147dc0121d252 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'show', '--no-all-versions', 'fsa'] 0m7.1s INFO: apt-cache knows about the following packages: fsa 0m7.1s INFO: Running scripts pre_install 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m7.3s 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: 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m7.3s DUMP: fsa: Installed: (none) Candidate: 1.15.9+dfsg-5 Version table: 1.15.9+dfsg-5 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa'] 0m10.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: exonerate gawk libgdbm-compat4 libgdbm6 libglib2.0-0 libmpfr6 libperl5.30 libreadline8 libsigsegv2 mummer perl perl-modules-5.30 readline-common Suggested packages: wise gawk-doc gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl readline-doc Recommended packages: med-config libglib2.0-data shared-mime-info xdg-user-dirs netbase The following NEW packages will be installed: exonerate fsa gawk libgdbm-compat4 libgdbm6 libglib2.0-0 libmpfr6 libperl5.30 libreadline8 libsigsegv2 mummer perl perl-modules-5.30 readline-common 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. Need to get 14.4 MB of archives. After this operation, 73.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.18.1-5.1 [64.4 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.18.1-5.1 [44.4 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.30.3-4 [290 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libmpfr6 amd64 4.1.0-3 [2012 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.0-4 [72.5 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 gawk amd64 1:5.0.1+dfsg-1 [610 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.2-1 [1363 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 exonerate amd64 2.4.0-4 [1544 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 mummer amd64 3.23+dfsg-6 [663 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 fsa amd64 1.15.9+dfsg-5 [700 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.4 MB in 0s (34.9 MB/s) Selecting previously unselected package perl-modules-5.30. (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 .../0-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.18.1-5.1_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-5.1) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.18.1-5.1_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-5.1) ... Selecting previously unselected package libperl5.30:amd64. Preparing to unpack .../3-libperl5.30_5.30.3-4_amd64.deb ... Unpacking libperl5.30:amd64 (5.30.3-4) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.30.3-4_amd64.deb ... Unpacking perl (5.30.3-4) ... Selecting previously unselected package libmpfr6:amd64. Preparing to unpack .../5-libmpfr6_4.1.0-3_amd64.deb ... Unpacking libmpfr6:amd64 (4.1.0-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../6-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../7-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../8-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Setting up libmpfr6:amd64 (4.1.0-3) ... Setting up readline-common (8.0-4) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package gawk. (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 ... 8644 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.0.1+dfsg-1_amd64.deb ... Unpacking gawk (1:5.0.1+dfsg-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.66.2-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.2-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../exonerate_2.4.0-4_amd64.deb ... Unpacking exonerate (2.4.0-4) ... Selecting previously unselected package mummer. Preparing to unpack .../mummer_3.23+dfsg-6_amd64.deb ... Unpacking mummer (3.23+dfsg-6) ... Selecting previously unselected package fsa. Preparing to unpack .../fsa_1.15.9+dfsg-5_amd64.deb ... Unpacking fsa (1.15.9+dfsg-5) ... Setting up perl-modules-5.30 (5.30.3-4) ... Setting up gawk (1:5.0.1+dfsg-1) ... Setting up libglib2.0-0:amd64 (2.66.2-1) ... No schema files found: doing nothing. Setting up exonerate (2.4.0-4) ... Setting up libgdbm6:amd64 (1.18.1-5.1) ... Setting up libgdbm-compat4:amd64 (1.18.1-5.1) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up perl (5.30.3-4) ... Setting up mummer (3.23+dfsg-6) ... Setting up fsa (1.15.9+dfsg-5) ... Processing triggers for libc-bin (2.31-4) ... 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa'] 0m10.4s INFO: Running scripts post_install 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m10.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m11.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m11.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpmejp_h84 to sid 0m11.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m11.0s INFO: Running scripts pre_distupgrade 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'update'] 0m15.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [146 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8505 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6407 kB] Fetched 15.1 MB in 3s (4402 kB/s) Reading package lists... 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'update'] 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-yf', 'dist-upgrade'] 0m18.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.32 perl-modules-5.32 The following packages will be upgraded: fsa gcc-10-base grep libffi7 libgcc-s1 libgmp10 libidn2-0 libreadline8 libstdc++6 perl perl-base readline-common 12 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 11.6 MB of archives. After this operation, 43.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 grep amd64 3.6-1 [398 kB] Get:2 http://deb.debian.org/debian sid/main amd64 perl-modules-5.32 all 5.32.0-5 [2821 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libperl5.32 amd64 5.32.0-5 [4119 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl amd64 5.32.0-5 [293 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.32.0-5 [1626 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 libffi7 amd64 3.3-5 [23.0 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.2.1+dfsg-1 [564 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.0-3 [86.0 kB] Get:12 http://deb.debian.org/debian sid/main amd64 readline-common all 8.1~rc2-2 [73.7 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.1~rc2-2 [168 kB] Get:14 http://deb.debian.org/debian sid/main amd64 fsa amd64 1.15.9+dfsg-6 [700 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.6 MB in 1s (17.9 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 ... 9087 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 ... 9088 files and directories currently installed.) Preparing to unpack .../perl_5.32.0-5_amd64.deb ... Unpacking perl (5.32.0-5) over (5.30.3-4) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../perl-modules-5.32_5.32.0-5_all.deb ... Unpacking perl-modules-5.32 (5.32.0-5) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../libperl5.32_5.32.0-5_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.0-5) ... 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 ... 11009 files and directories currently installed.) 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 ... 11009 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 ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11010 files and directories currently installed.) Preparing to unpack .../readline-common_8.1~rc2-2_all.deb ... Unpacking readline-common (8.1~rc2-2) over (8.0-4) ... Preparing to unpack .../libreadline8_8.1~rc2-2_amd64.deb ... Unpacking libreadline8:amd64 (8.1~rc2-2) over (8.0-4) ... Preparing to unpack .../fsa_1.15.9+dfsg-6_amd64.deb ... Unpacking fsa (1.15.9+dfsg-6) over (1.15.9+dfsg-5) ... Setting up perl-modules-5.32 (5.32.0-5) ... Setting up fsa (1.15.9+dfsg-6) ... Setting up libperl5.32:amd64 (5.32.0-5) ... Setting up readline-common (8.1~rc2-2) ... Setting up libreadline8:amd64 (8.1~rc2-2) ... Setting up perl (5.32.0-5) ... Processing triggers for libc-bin (2.31-4) ... 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-yf', 'dist-upgrade'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.5s DUMP: 6bbf8d9941540f25a61652bd5fa6780a - 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'show', '--no-all-versions', 'fsa'] 0m18.7s DUMP: Package: fsa Version: 1.15.9+dfsg-6 Installed-Size: 4254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2), mummer, exonerate Recommends: med-config (>= 2.1) Description-en: Fast Statistical Alignment of protein, RNA or DNA sequences FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz. . FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments: * FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints. * FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy. * FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above. * The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned Description-md5: 6250169bc99ea71aef4983021689c512 Homepage: http://fsa.sourceforge.net/ Section: science Priority: optional Filename: pool/main/f/fsa/fsa_1.15.9+dfsg-6_amd64.deb Size: 699936 MD5sum: 3a5a89e181ad156b3a5b981f38c9b0f0 SHA256: fe5b2aa4210ef3a1e676108a160416106354054310d47c01d8262fefb6255bb3 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'show', '--no-all-versions', 'fsa'] 0m18.7s INFO: apt-cache knows about the following packages: fsa 0m18.7s INFO: Running scripts pre_install 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m18.8s 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: 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m18.8s DUMP: fsa: Installed: 1.15.9+dfsg-6 Candidate: 1.15.9+dfsg-6 Version table: *** 1.15.9+dfsg-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa'] 0m19.3s DUMP: Reading package lists... Building dependency tree... Reading state information... fsa is already the newest version (1.15.9+dfsg-6). The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa'] 0m19.3s INFO: Running scripts post_install 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m19.3s INFO: Running scripts post_distupgrade 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m20.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m20.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m20.7s INFO: Running scripts pre_install 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_database-server'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_exceptions'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_extras'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m20.8s 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: 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m20.8s DUMP: fsa: Installed: 1.15.9+dfsg-6 Candidate: 1.15.9+dfsg-6 Version table: *** 1.15.9+dfsg-6 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-cache', 'policy', 'fsa'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa=1.15.9+dfsg-6'] 0m21.2s DUMP: Reading package lists... Building dependency tree... Reading state information... fsa is already the newest version (1.15.9+dfsg-6). The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', '-y', 'install', 'fsa=1.15.9+dfsg-6'] 0m21.2s INFO: Running scripts post_install 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_install_exceptions'] 0m21.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m21.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m22.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', '-ac', '--ignore-obsolete'] 0m23.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', '-ac', '--ignore-obsolete'] 0m23.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.4s DUMP: 0.15.2 0m23.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m23.4s INFO: Running adequate version 0.15.2 now. 0m23.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'fsa'] 0m23.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'fsa'] 0m23.5s INFO: Running scripts pre_remove 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/pre_remove_exceptions'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.6s 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 exonerate exonerate 2.4.0-4 install ok installed findutils findutils 4.7.0+git20201010-2 install ok installed fsa fsa 1.15.9+dfsg-6 install ok installed gawk gawk 1:5.0.1+dfsg-1 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 2.36-3+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 3.3-5 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 libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-5.1 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-5.1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.2-1 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 2.36-3+b2 install ok installed libmpfr6:amd64 libmpfr6 4.1.0-3 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 libperl5.30:amd64 libperl5.30 5.30.3-4 install ok installed libperl5.32:amd64 libperl5.32 5.32.0-5 install ok installed libreadline8:amd64 libreadline8 8.1~rc2-2 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 libsigsegv2:amd64 libsigsegv2 2.12-2 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 10.2.0-17 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 2.36-3+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 mummer mummer 3.23+dfsg-6 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 perl 5.32.0-5 install ok installed perl-base perl-base 5.32.0-5 install ok installed perl-modules-5.30 perl-modules-5.30 5.30.3-4 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.0-5 install ok installed readline-common readline-common 8.1~rc2-2 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 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'remove', 'exonerate', 'gawk', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libglib2.0-0:amd64', 'libmpfr6:amd64', 'libperl5.30:amd64', 'libperl5.32:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'mummer', 'perl', 'perl-modules-5.30', 'perl-modules-5.32', 'readline-common', 'fsa'] 0m25.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: exonerate fsa gawk libgdbm-compat4 libgdbm6 libglib2.0-0 libmpfr6 libperl5.30 libperl5.32 libreadline8 libsigsegv2 mummer perl perl-modules-5.30 perl-modules-5.32 readline-common 0 upgraded, 0 newly installed, 16 to remove and 0 not upgraded. After this operation, 120 MB 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 ... 11010 files and directories currently installed.) Removing fsa (1.15.9+dfsg-6) ... Removing exonerate (2.4.0-4) ... Removing mummer (3.23+dfsg-6) ... Removing gawk (1:5.0.1+dfsg-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libperl5.30:amd64 (5.30.3-4) ... Removing perl (5.32.0-5) ... Removing libperl5.32:amd64 (5.32.0-5) ... Removing libgdbm-compat4:amd64 (1.18.1-5.1) ... Removing libgdbm6:amd64 (1.18.1-5.1) ... Removing libglib2.0-0:amd64 (2.66.2-1) ... Removing libmpfr6:amd64 (4.1.0-3) ... Removing libreadline8:amd64 (8.1~rc2-2) ... Removing libsigsegv2:amd64 (2.12-2) ... Removing perl-modules-5.30 (5.30.3-4) ... Removing perl-modules-5.32 (5.32.0-5) ... Removing readline-common (8.1~rc2-2) ... Processing triggers for libc-bin (2.31-4) ... 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'remove', 'exonerate', 'gawk', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libglib2.0-0:amd64', 'libmpfr6:amd64', 'libperl5.30:amd64', 'libperl5.32:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'mummer', 'perl', 'perl-modules-5.30', 'perl-modules-5.32', 'readline-common', 'fsa'] 0m25.3s INFO: Running scripts post_remove 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_remove_exceptions'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_remove_exceptions'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', 'exonerate', 'gawk', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libglib2.0-0:amd64', 'libmpfr6:amd64', 'libperl5.30:amd64', 'libperl5.32:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'mummer', 'perl', 'perl-modules-5.30', 'perl-modules-5.32', 'readline-common'] 0m25.3s DUMP: dpkg: warning: ignoring request to remove exonerate which isn't installed (Reading database ... 6688 files and directories currently installed.) Purging configuration files for gawk (1:5.0.1+dfsg-1) ... dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.66.2-1) ... dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libperl5.30 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for perl (5.32.0-5) ... dpkg: warning: ignoring request to remove perl-modules-5.30 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for readline-common (8.1~rc2-2) ... 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', 'exonerate', 'gawk', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libglib2.0-0:amd64', 'libmpfr6:amd64', 'libperl5.30:amd64', 'libperl5.32:amd64', 'libreadline8:amd64', 'libsigsegv2:amd64', 'mummer', 'perl', 'perl-modules-5.30', 'perl-modules-5.32', 'readline-common'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', 'fsa'] 0m25.3s DUMP: dpkg: warning: ignoring request to remove fsa which isn't installed 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', 'fsa'] 0m25.3s INFO: Running scripts post_purge 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_purge_exceptions'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_purge_exceptions'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', '--pending'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--purge', '--pending'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--remove', '--pending'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg', '--remove', '--pending'] 0m25.4s INFO: Running scripts post_test 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_test_exceptions'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'tmp/scripts/post_test_exceptions'] 0m25.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m25.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-divert', '--list'] 0m25.7s 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 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'dpkg-divert', '--list'] 0m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'clean'] 0m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmejp_h84', 'apt-get', 'clean'] 0m25.7s DEBUG: Recording chroot state 0m26.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/shm'] 0m26.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/shm'] 0m26.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/console'] 0m26.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/console'] 0m26.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/ptmx'] 0m26.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/ptmx'] 0m26.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts'] 0m26.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/dev/pts'] 0m26.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/proc'] 0m26.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmejp_h84/proc'] 0m26.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m26.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmejp_h84'] 0m26.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmejp_h84 0m26.6s INFO: PASS: Upgrading between Debian distributions. 0m26.6s INFO: PASS: All tests. 0m26.6s INFO: piuparts run ends. ret=0 End: 2020-11-15 20:51:13 GMT