Start: 2025-08-17 01:00:54 GMT Package: ruby-bio Version: 2.0.5-1 Installed-Size: 2804 Maintainer: Debian Ruby Team Architecture: all Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Breaks: ruby-crb-blast (<< 0.6.9-4) Description: Ruby tools for computational molecular biology Homepage: https://bioruby.org/ Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_2.0.5-1_all.deb Size: 656832 MD5sum: 6b30eeea4b84581b7c9732444564d65b SHA256: 9f50f668237d86011e1cb40b1f1bb964dfb322d827a0a1a7423df712652ac5f3 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --install-recommends --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/forky-merged-usr_amd64.tar.gz -d forky --no-upgrade-test --apt ruby-bio=2.0.5-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508101417~1.6.0-7-g17c4ea32 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-recommends --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/forky-merged-usr_amd64.tar.gz -d forky --no-upgrade-test --apt ruby-bio=2.0.5-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-38-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.147-1 (2025-08-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmphu546fwf 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmphu546fwf 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphu546fwf', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphu546fwf', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphu546fwf/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphu546fwf/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmphu546fwf/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'update'] 0m3.2s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [145 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9728 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6528 kB] Fetched 16.4 MB in 1s (11.9 MB/s) Reading package lists... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'update'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', '-yf', 'dist-upgrade'] 0m4.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libaudit-common libaudit1 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 146 kB of archives. After this operation, 26.6 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.0.5-1 [13.5 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.0.5-1 [59.4 kB] Fetched 146 kB in 0s (4720 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 ... 4934 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 4933 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.0.5-1_all.deb ... Unpacking libaudit-common (1:4.0.5-1) over (1:4.0.2-2) ... Setting up libaudit-common (1:4.0.5-1) ... (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 ... 4933 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.5-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.5-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.0.5-1) ... Processing triggers for libc-bin (2.41-12) ... 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', '-yf', 'dist-upgrade'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s DUMP: 10936186b1a6b7fc2a66bfcad138066a - 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s INFO: Running scripts post_setup 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_dummy_users'] 0m5.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_dummy_users'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_forbid_home'] 0m5.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_forbid_home'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_minimize'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_minimize'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_zz_backports'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_setup_zz_backports'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'clean'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'clean'] 0m5.9s DEBUG: Recording chroot state 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.5-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.5-1 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-divert', '--list'] 0m6.4s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-divert', '--list'] 0m6.4s INFO: Running scripts is_testable 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/is_testable_uninstallable'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/is_testable_uninstallable'] 0m6.4s INFO: apt-cache does not know about any of the requested packages 0m6.4s INFO: Running scripts pre_test 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_test_exceptions'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_test_exceptions'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_test_root_password'] 0m6.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_test_root_password'] 0m6.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m7.0s DEBUG: No broken symlinks as far as we can find. 0m7.0s INFO: Running scripts pre_install 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m7.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m7.5s DEBUG: No broken symlinks as far as we can find. 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-cache', 'policy'] 0m8.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-cache', 'policy'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-cache', 'policy', 'ruby-bio'] 0m8.3s DUMP: ruby-bio: Installed: (none) Candidate: 2.0.5-1 Version table: 2.0.5-1 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-cache', 'policy', 'ruby-bio'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', '-y', 'install', 'ruby-bio=2.0.5-1'] 0m27.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libatomic1 libauthen-sasl-perl libbrotli1 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libencode-locale-perl libexpat1 libfcgi-bin libfcgi-perl libfcgi0t64 libffi8 libfile-listing-perl libfont-afm-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgnutls30t64 libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmime-tools-perl libmpfr6 libncbi-vdb3 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnghttp2-14 libp11-kit0 libperl5.40 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libruby libruby3.3 libsigsegv2 libsoap-lite-perl libtask-weaken-perl libtasn1-6 libtext-charwidth-perl libtext-wrapi18n-perl libtimedate-perl libtry-tiny-perl libunistring5 liburi-perl libuv1t64 libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 linux-sysctl-defaults lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data ncbi-vdb-data netbase openssl perl perl-modules-5.40 perl-openssl-defaults poa prank probcons procps proda psmisc python3 python3-minimal python3.13 python3.13-minimal rake readline-common ruby ruby-csv ruby-did-you-mean ruby-net-telnet ruby-ruby2-keywords ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.3 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip Suggested packages: liblocale-gettext-perl cron quota blends-doc bzip2-doc clustalx seaview wise gawk-doc hmmer-doc apache2 | lighttpd | httpd libdigest-hmac-perl libgssapi-perl gdbm-l10n low-memory-monitor gnutls-bin gpm libcrypt-ssleay-perl libapache2-mod-perl2 libmime-lite-perl libnet-jabber-perl libsub-name-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl libxml-sax-expatxs-perl menu-l10n mustang-testdata perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl debhelper blast2 probcons-extra python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binutils binfmt-support readline-doc ri ruby-dev emboss bundler boxshade t-coffee-examples pymol rasmol Recommended packages: blast2 The following NEW packages will be installed: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libatomic1 libauthen-sasl-perl libbrotli1 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libencode-locale-perl libexpat1 libfcgi-bin libfcgi-perl libfcgi0t64 libffi8 libfile-listing-perl libfont-afm-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgnutls30t64 libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmime-tools-perl libmpfr6 libncbi-vdb3 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnghttp2-14 libp11-kit0 libperl5.40 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libruby libruby3.3 libsigsegv2 libsoap-lite-perl libtask-weaken-perl libtasn1-6 libtext-charwidth-perl libtext-wrapi18n-perl libtimedate-perl libtry-tiny-perl libunistring5 liburi-perl libuv1t64 libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 linux-sysctl-defaults lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data ncbi-vdb-data netbase openssl perl perl-modules-5.40 perl-openssl-defaults poa prank probcons procps proda psmisc python3 python3-minimal python3.13 python3.13-minimal rake readline-common ruby ruby-bio ruby-csv ruby-did-you-mean ruby-net-telnet ruby-ruby2-keywords ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.3 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip 0 upgraded, 161 newly installed, 0 to remove and 0 not upgraded. Need to get 77.9 MB of archives. After this operation, 362 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Get:3 http://deb.debian.org/debian forky/main amd64 readline-common all 8.2-6 [69.4 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libsigsegv2 amd64 2.14-1+b2 [34.4 kB] Get:6 http://deb.debian.org/debian forky/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:9 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:10 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:11 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get:12 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get:13 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:15 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:16 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:18 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:19 http://deb.debian.org/debian forky/main amd64 adduser all 3.152 [191 kB] Get:20 http://deb.debian.org/debian forky/main amd64 linux-sysctl-defaults all 4.14 [5756 B] Get:21 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:22 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:23 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:24 http://deb.debian.org/debian forky/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Get:25 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.1-1 [1494 kB] Get:26 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get:27 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:29 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:30 http://deb.debian.org/debian forky/main amd64 perl-modules-5.40 all 5.40.1-6 [3019 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:32 http://deb.debian.org/debian forky/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libperl5.40 amd64 5.40.1-6 [4341 kB] Get:34 http://deb.debian.org/debian forky/main amd64 perl amd64 5.40.1-6 [267 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:36 http://deb.debian.org/debian forky/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:37 http://deb.debian.org/debian forky/main amd64 ucf all 3.0052 [43.3 kB] Get:38 http://deb.debian.org/debian forky/main amd64 xz-utils amd64 5.8.1-1 [660 kB] Get:39 http://deb.debian.org/debian forky/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get:40 http://deb.debian.org/debian forky/main amd64 menu amd64 2.1.51 [355 kB] Get:41 http://deb.debian.org/debian forky/main amd64 blends-common all 0.7.10 [15.0 kB] Get:42 http://deb.debian.org/debian forky/main amd64 libargtable2-0 amd64 13-4 [18.1 kB] Get:43 http://deb.debian.org/debian forky/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:44 http://deb.debian.org/debian forky/main amd64 clustalo amd64 1.2.4-8 [267 kB] Get:45 http://deb.debian.org/debian forky/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get:46 http://deb.debian.org/debian forky/main amd64 dialign-tx-data all 1.0.2-15 [862 kB] Get:47 http://deb.debian.org/debian forky/main amd64 dialign-tx amd64 1.0.2-15 [87.6 kB] Get:48 http://deb.debian.org/debian forky/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:49 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.84.3-1 [1515 kB] Get:50 http://deb.debian.org/debian forky/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] Get:51 http://deb.debian.org/debian forky/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:52 http://deb.debian.org/debian forky/main amd64 fsa amd64 1.15.9+dfsg-6 [700 kB] Get:53 http://deb.debian.org/debian forky/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get:54 http://deb.debian.org/debian forky/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:55 http://deb.debian.org/debian forky/main amd64 javascript-common all 12+nmu1 [4864 B] Get:56 http://deb.debian.org/debian forky/main amd64 kalign amd64 1:3.4.0-1+b3 [138 kB] Get:57 http://deb.debian.org/debian forky/main amd64 libauthen-sasl-perl all 2.1700-1 [44.8 kB] Get:58 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:59 http://deb.debian.org/debian forky/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:60 http://deb.debian.org/debian forky/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get:61 http://deb.debian.org/debian forky/main amd64 libconvert-binhex-perl all 1.125-3 [27.4 kB] Get:62 http://deb.debian.org/debian forky/main amd64 libdata-dump-perl all 1.25-1 [28.4 kB] Get:63 http://deb.debian.org/debian forky/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:64 http://deb.debian.org/debian forky/main amd64 libfcgi0t64 amd64 2.4.5-0.1 [25.4 kB] Get:65 http://deb.debian.org/debian forky/main amd64 libfcgi-bin amd64 2.4.5-0.1 [12.4 kB] Get:66 http://deb.debian.org/debian forky/main amd64 libfcgi-perl amd64 0.82+ds-3+b2 [25.3 kB] Get:67 http://deb.debian.org/debian forky/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:68 http://deb.debian.org/debian forky/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:69 http://deb.debian.org/debian forky/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:70 http://deb.debian.org/debian forky/main amd64 libfont-afm-perl all 1.20-4 [13.1 kB] Get:71 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:72 http://deb.debian.org/debian forky/main amd64 libglib2.0-data all 2.84.3-1 [1285 kB] Get:73 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:74 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:75 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:76 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:77 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get:78 http://deb.debian.org/debian forky/main amd64 libgpm2 amd64 1.20.7-11+b2 [14.4 kB] Get:79 http://deb.debian.org/debian forky/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:80 http://deb.debian.org/debian forky/main amd64 liburi-perl all 5.30-1 [105 kB] Get:81 http://deb.debian.org/debian forky/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get:82 http://deb.debian.org/debian forky/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:83 http://deb.debian.org/debian forky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:84 http://deb.debian.org/debian forky/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get:85 http://deb.debian.org/debian forky/main amd64 libhtml-form-perl all 6.12-1 [32.3 kB] Get:86 http://deb.debian.org/debian forky/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:87 http://deb.debian.org/debian forky/main amd64 libhtml-format-perl all 2.16-2 [38.8 kB] Get:88 http://deb.debian.org/debian forky/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:89 http://deb.debian.org/debian forky/main amd64 libhttp-daemon-perl all 6.16-1 [23.5 kB] Get:90 http://deb.debian.org/debian forky/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:91 http://deb.debian.org/debian forky/main amd64 libio-compress-brotli-perl amd64 0.004001-2+b3 [16.9 kB] Get:92 http://deb.debian.org/debian forky/main amd64 libio-sessiondata-perl all 1.03-3 [6316 B] Get:93 http://deb.debian.org/debian forky/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:94 http://deb.debian.org/debian forky/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get:95 http://deb.debian.org/debian forky/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get:96 http://deb.debian.org/debian forky/main amd64 libio-stringy-perl all 2.113-2 [48.3 kB] Get:97 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:98 http://deb.debian.org/debian forky/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:99 http://deb.debian.org/debian forky/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:100 http://deb.debian.org/debian forky/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:101 http://deb.debian.org/debian forky/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:102 http://deb.debian.org/debian forky/main amd64 libwww-perl all 6.78-1 [183 kB] Get:103 http://deb.debian.org/debian forky/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:104 http://deb.debian.org/debian forky/main amd64 libnet-smtp-ssl-perl all 1.04-2 [6548 B] Get:105 http://deb.debian.org/debian forky/main amd64 libmailtools-perl all 2.22-1 [88.8 kB] Get:106 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get:107 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get:108 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get:109 http://deb.debian.org/debian forky/main amd64 libmime-tools-perl all 5.515-1 [203 kB] Get:110 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:111 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:112 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:113 http://deb.debian.org/debian forky/main amd64 rubygems-integration all 1.19 [5488 B] Get:114 http://deb.debian.org/debian forky/main amd64 ruby3.3 amd64 3.3.8-2 [834 kB] Get:115 http://deb.debian.org/debian forky/main amd64 ruby-rubygems all 3.6.7-2 [407 kB] Get:116 http://deb.debian.org/debian forky/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get:117 http://deb.debian.org/debian forky/main amd64 rake all 13.2.1-1 [65.2 kB] Get:118 http://deb.debian.org/debian forky/main amd64 ruby-csv all 3.3.4-1 [42.2 kB] Get:119 http://deb.debian.org/debian forky/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get:120 http://deb.debian.org/debian forky/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:121 http://deb.debian.org/debian forky/main amd64 ruby-ruby2-keywords all 0.0.5-1 [4300 B] Get:122 http://deb.debian.org/debian forky/main amd64 ruby-webrick all 1.9.1-1 [59.6 kB] Get:123 http://deb.debian.org/debian forky/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:124 http://deb.debian.org/debian forky/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:125 http://deb.debian.org/debian forky/main amd64 libruby3.3 amd64 3.3.8-2 [6301 kB] Get:126 http://deb.debian.org/debian forky/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get:127 http://deb.debian.org/debian forky/main amd64 libtask-weaken-perl all 1.06-2 [9364 B] Get:128 http://deb.debian.org/debian forky/main amd64 libxml-parser-perl amd64 2.47-1+b3 [198 kB] Get:129 http://deb.debian.org/debian forky/main amd64 libsoap-lite-perl all 1.27-3 [239 kB] Get:130 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:131 http://deb.debian.org/debian forky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get:132 http://deb.debian.org/debian forky/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:133 http://deb.debian.org/debian forky/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:134 http://deb.debian.org/debian forky/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:135 http://deb.debian.org/debian forky/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b2 [314 kB] Get:136 http://deb.debian.org/debian forky/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] Get:137 http://deb.debian.org/debian forky/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:138 http://deb.debian.org/debian forky/main amd64 libxmlrpc-lite-perl all 0.717-5 [22.4 kB] Get:139 http://deb.debian.org/debian forky/main amd64 lynx-common all 2.9.2-1 [1193 kB] Get:140 http://deb.debian.org/debian forky/main amd64 lynx amd64 2.9.2-1 [641 kB] Get:141 http://deb.debian.org/debian forky/main amd64 mafft amd64 7.505-1 [1078 kB] Get:142 http://deb.debian.org/debian forky/main amd64 mailcap all 3.74 [32.8 kB] Get:143 http://deb.debian.org/debian forky/main amd64 med-config all 3.9.0 [11.6 kB] Get:144 http://deb.debian.org/debian forky/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get:145 http://deb.debian.org/debian forky/main amd64 mustang amd64 3.2.4-1 [105 kB] Get:146 http://deb.debian.org/debian forky/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:147 http://deb.debian.org/debian forky/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Get:148 http://deb.debian.org/debian forky/main amd64 poa amd64 2.0+20060928-10 [53.4 kB] Get:149 http://deb.debian.org/debian forky/main amd64 prank amd64 0.0.170427+dfsg-3 [395 kB] Get:150 http://deb.debian.org/debian forky/main amd64 probcons amd64 1.12-14 [119 kB] Get:151 http://deb.debian.org/debian forky/main amd64 proda amd64 1.0-14 [65.4 kB] Get:152 http://deb.debian.org/debian forky/main amd64 psmisc amd64 23.7-2 [267 kB] Get:153 http://deb.debian.org/debian forky/main amd64 ruby-bio all 2.0.5-1 [657 kB] Get:154 http://deb.debian.org/debian forky/main amd64 ruby-sdbm amd64 1.0.0-5+b7 [15.1 kB] Get:155 http://deb.debian.org/debian forky/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get:156 http://deb.debian.org/debian forky/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] Get:157 http://deb.debian.org/debian forky/main amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [1032 kB] Get:158 http://deb.debian.org/debian forky/main amd64 tm-align amd64 20190822+dfsg-3 [867 kB] Get:159 http://deb.debian.org/debian forky/main amd64 unzip amd64 6.0-29 [173 kB] Get:160 http://deb.debian.org/debian forky/main amd64 xdg-user-dirs amd64 0.18-2 [53.2 kB] Get:161 http://deb.debian.org/debian forky/main amd64 zip amd64 3.0-15 [235 kB] Preconfiguring packages ... Fetched 77.9 MB in 1s (138 MB/s) Selecting previously unselected package fonts-lato. (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 ... 4936 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libmpfr6:amd64. Preparing to unpack .../libmpfr6_4.2.2-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.2.2-1) ... Selecting previously unselected package readline-common. 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Unpacking libmailtools-perl (2.22-1) ... Selecting previously unselected package libmbedcrypto16:amd64. Preparing to unpack .../086-libmbedcrypto16_3.6.4-2_amd64.deb ... Unpacking libmbedcrypto16:amd64 (3.6.4-2) ... Selecting previously unselected package libmbedx509-7:amd64. Preparing to unpack .../087-libmbedx509-7_3.6.4-2_amd64.deb ... Unpacking libmbedx509-7:amd64 (3.6.4-2) ... Selecting previously unselected package libmbedtls21:amd64. Preparing to unpack .../088-libmbedtls21_3.6.4-2_amd64.deb ... Unpacking libmbedtls21:amd64 (3.6.4-2) ... Selecting previously unselected package libmime-tools-perl. Preparing to unpack .../089-libmime-tools-perl_5.515-1_all.deb ... Unpacking libmime-tools-perl (5.515-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../090-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. 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Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-csv. Preparing to unpack .../098-ruby-csv_3.3.4-1_all.deb ... Unpacking ruby-csv (3.3.4-1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../099-ruby-did-you-mean_1.6.3-2_all.deb ... Unpacking ruby-did-you-mean (1.6.3-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../100-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-ruby2-keywords. Preparing to unpack .../101-ruby-ruby2-keywords_0.0.5-1_all.deb ... Unpacking ruby-ruby2-keywords (0.0.5-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../102-ruby-webrick_1.9.1-1_all.deb ... Unpacking ruby-webrick (1.9.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../103-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../104-libyaml-0-2_0.2.5-2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-2) ... Selecting previously unselected package libruby3.3:amd64. Preparing to unpack .../105-libruby3.3_3.3.8-2_amd64.deb ... Unpacking libruby3.3:amd64 (3.3.8-2) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../106-libruby_1%3a3.3+b1_amd64.deb ... Unpacking libruby:amd64 (1:3.3+b1) ... Selecting previously unselected package libtask-weaken-perl. Preparing to unpack .../107-libtask-weaken-perl_1.06-2_all.deb ... Unpacking libtask-weaken-perl (1.06-2) ... Selecting previously unselected package libxml-parser-perl. Preparing to unpack .../108-libxml-parser-perl_2.47-1+b3_amd64.deb ... Unpacking libxml-parser-perl (2.47-1+b3) ... Selecting previously unselected package libsoap-lite-perl. Preparing to unpack .../109-libsoap-lite-perl_1.27-3_all.deb ... Unpacking libsoap-lite-perl (1.27-3) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../110-libuv1t64_1.50.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.50.0-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../111-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../112-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../113-libxml-sax-base-perl_1.09-3_all.deb ... Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../114-libxml-sax-perl_1.02+dfsg-4_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-4) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../115-libxml-libxml-perl_2.0207+dfsg+really+2.0134-5+b2_amd64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b2) ... Selecting previously unselected package libxml-sax-expat-perl. Preparing to unpack .../116-libxml-sax-expat-perl_0.51-2_all.deb ... Unpacking libxml-sax-expat-perl (0.51-2) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../117-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libxmlrpc-lite-perl. Preparing to unpack .../118-libxmlrpc-lite-perl_0.717-5_all.deb ... Unpacking libxmlrpc-lite-perl (0.717-5) ... Selecting previously unselected package lynx-common. Preparing to unpack .../119-lynx-common_2.9.2-1_all.deb ... Unpacking lynx-common (2.9.2-1) ... Selecting previously unselected package lynx. Preparing to unpack .../120-lynx_2.9.2-1_amd64.deb ... Unpacking lynx (2.9.2-1) ... Selecting previously unselected package mafft. Preparing to unpack .../121-mafft_7.505-1_amd64.deb ... Unpacking mafft (7.505-1) ... Selecting previously unselected package mailcap. Preparing to unpack .../122-mailcap_3.74_all.deb ... Unpacking mailcap (3.74) ... Selecting previously unselected package med-config. Preparing to unpack .../123-med-config_3.9.0_all.deb ... Unpacking med-config (3.9.0) ... Selecting previously unselected package muscle. Preparing to unpack .../124-muscle_1%3a5.1.0-1_amd64.deb ... Unpacking muscle (1:5.1.0-1) ... Selecting previously unselected package mustang. Preparing to unpack .../125-mustang_3.2.4-1_amd64.deb ... Unpacking mustang (3.2.4-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../126-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../127-ncbi-blast+_2.16.0+ds-7_amd64.deb ... Unpacking ncbi-blast+ (2.16.0+ds-7) ... Selecting previously unselected package poa. Preparing to unpack .../128-poa_2.0+20060928-10_amd64.deb ... Unpacking poa (2.0+20060928-10) ... Selecting previously unselected package prank. Preparing to unpack .../129-prank_0.0.170427+dfsg-3_amd64.deb ... Unpacking prank (0.0.170427+dfsg-3) ... Selecting previously unselected package probcons. Preparing to unpack .../130-probcons_1.12-14_amd64.deb ... Unpacking probcons (1.12-14) ... Selecting previously unselected package proda. Preparing to unpack .../131-proda_1.0-14_amd64.deb ... Unpacking proda (1.0-14) ... Selecting previously unselected package psmisc. Preparing to unpack .../132-psmisc_23.7-2_amd64.deb ... Unpacking psmisc (23.7-2) ... Selecting previously unselected package ruby-bio. Preparing to unpack .../133-ruby-bio_2.0.5-1_all.deb ... Unpacking ruby-bio (2.0.5-1) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../134-ruby-sdbm_1.0.0-5+b7_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b7) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../135-shared-mime-info_2.4-5+b2_amd64.deb ... Unpacking shared-mime-info (2.4-5+b2) ... Selecting previously unselected package sim4. Preparing to unpack .../136-sim4_0.0.20121010-8_amd64.deb ... Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package t-coffee. Preparing to unpack .../137-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Selecting previously unselected package tm-align. Preparing to unpack .../138-tm-align_20190822+dfsg-3_amd64.deb ... Unpacking tm-align (20190822+dfsg-3) ... Selecting previously unselected package unzip. Preparing to unpack .../139-unzip_6.0-29_amd64.deb ... Unpacking unzip (6.0-29) ... Selecting previously unselected package xdg-user-dirs. Preparing to unpack .../140-xdg-user-dirs_0.18-2_amd64.deb ... Unpacking xdg-user-dirs (0.18-2) ... Selecting previously unselected package zip. Preparing to unpack .../141-zip_3.0-15_amd64.deb ... Unpacking zip (3.0-15) ... Setting up media-types (13.0.0) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up javascript-common (12+nmu1) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up ruby-ruby2-keywords (0.0.5-1) ... Setting up fonts-lato (2.015-1) ... Setting up libgpm2:amd64 (1.20.7-11+b2) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up probcons (1.12-14) ... Setting up poa (2.0+20060928-10) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up xdg-user-dirs (0.18-2) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up psmisc (23.7-2) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libfcgi0t64:amd64 (2.4.5-0.1) ... Setting up unzip (6.0-29) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libfcgi-bin (2.4.5-0.1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up file (1:5.46-5) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up muscle (1:5.1.0-1) ... Setting up bzip2 (1.0.8-6) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Setting up zip (3.0-15) ... Setting up kalign (1:3.4.0-1+b3) ... Setting up libglib2.0-data (2.84.3-1) ... Setting up linux-sysctl-defaults (4.14) ... Setting up dialign-tx-data (1.0.2-15) ... Setting up mustang (3.2.4-1) ... Setting up proda (1.0-14) ... Setting up sim4 (0.0.20121010-8) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up xz-utils (5.8.1-1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up ruby-csv (3.3.4-1) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up lynx-common (2.9.2-1) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up ruby-webrick (1.9.1-1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up perl-modules-5.40 (5.40.1-6) ... Setting up sensible-utils (0.0.25) ... Setting up dialign-tx (1.0.2-15) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up clustalw (2.1+lgpl-7) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up ruby-did-you-mean (1.6.3-2) ... Setting up menu (2.1.51) ... Setting up libdivsufsort3:amd64 (2.0.1-6+b1) ... Setting up openssl (3.5.1-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up prank (0.0.170427+dfsg-3) ... Setting up libargtable2-0:amd64 (13-4) ... Setting up ruby-bio (2.0.5-1) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.5-1) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up clustalo (1.2.4-8) ... Setting up tm-align (20190822+dfsg-3) ... Setting up libperl5.40:amd64 (5.40.1-6) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up perl (5.40.1-6) ... Setting up libglib2.0-0t64:amd64 (2.84.3-1) ... No schema files found: doing nothing. Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libdata-dump-perl (1.25-1) ... Setting up libio-compress-brotli-perl (0.004001-2+b3) ... Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libio-html-perl (1.004-3) ... Setting up ucf (3.0052) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up mummer (3.23+dfsg-8) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libfcgi-perl (0.82+ds-3+b2) ... Setting up mailcap (3.74) ... Setting up exonerate (2.4.0-5+b1) ... Setting up liburi-perl (5.30-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libio-sessiondata-perl (1.03-3) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libtask-weaken-perl (1.06-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libfont-afm-perl (1.20-4) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.47-1+b1) ... Setting up libio-stringy-perl (2.113-2) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libauthen-sasl-perl (2.1700-1) ... Setting up libconvert-binhex-perl (1.125-3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libnet-http-perl (6.23-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up rubygems-integration (1.19) ... Setting up fsa (1.15.9+dfsg-6) ... Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up lynx (2.9.2-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libio-socket-ssl-perl (2.089-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libhtml-form-perl (6.12-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libhtml-format-perl (2.16-2) ... Setting up libxml-sax-perl (1.02+dfsg-4) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libnet-smtp-ssl-perl (1.04-2) ... Setting up libmailtools-perl (2.22-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libhttp-daemon-perl (6.16-1) ... Setting up libmime-tools-perl (5.515-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up libwww-perl (6.78-1) ... Setting up ruby-rubygems (3.6.7-2) ... Setting up ruby (1:3.3+b1) ... Setting up rake (13.2.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up libruby3.3:amd64 (3.3.8-2) ... Setting up libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up ruby3.3 (3.3.8-2) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b7) ... Setting up libsoap-lite-perl (1.27-3) ... Setting up libxmlrpc-lite-perl (0.717-5) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for menu (2.1.51) ... Setting up blends-common (0.7.10) ... Setting up med-config (3.9.0) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', '-y', 'install', 'ruby-bio=2.0.5-1'] 0m27.6s INFO: Running scripts post_install 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_install_exceptions'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_install_exceptions'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'systemd-tmpfiles', '--cat-config'] 0m27.6s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 0m27.6s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'systemd-tmpfiles', '--cat-config'] 0m27.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m28.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m29.5s ERROR: WARN: Broken symlinks: /usr/share/man/man1/rdbg.1.gz -> rdbg3.3.1.gz (ruby) 0m30.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphu546fwf', '-ac', '--ignore-obsolete'] 0m32.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphu546fwf', '-ac', '--ignore-obsolete'] 0m32.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.2s DUMP: 0.15.9~deb12u1 0m32.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m32.2s INFO: Running adequate version 0.15.9~deb12u1 now. 0m32.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'ruby-bio'] 0m32.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'ruby-bio'] 0m32.3s INFO: Running scripts pre_remove 0m32.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/pre_remove_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m34.0s DUMP: install ok installed adduser adduser 3.152 install ok installed amap-align amap-align 2.2+git20080214.600fc29+dfsg-2 install ok installed apt apt 3.0.3 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed blends-common blends-common 0.7.10 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed bzip2 bzip2 1.0.8-6 install ok installed ca-certificates ca-certificates 20250419 install ok installed clustalo clustalo 1.2.4-8 install ok installed clustalw clustalw 2.1+lgpl-7 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed dialign-tx dialign-tx 1.0.2-15 install ok installed dialign-tx-data dialign-tx-data 1.0.2-15 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed exonerate exonerate 2.4.0-5+b1 install ok installed file file 1:5.46-5 install ok installed findutils findutils 4.10.0-3 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fsa fsa 1.15.9+dfsg-6 install ok installed gawk gawk 1:5.2.1-2+b1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hmmer hmmer 3.4+dfsg-2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed javascript-common javascript-common 12+nmu1 install ok installed kalign kalign 1:3.4.0-1+b3 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libargtable2-0:amd64 libargtable2-0 13-4 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.5-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.5-1 install ok installed libauthen-sasl-perl libauthen-sasl-perl 2.1700-1 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libclass-inspector-perl libclass-inspector-perl 1.36-3 install ok installed libclone-perl:amd64 libclone-perl 0.47-1+b1 install ok installed libconvert-binhex-perl libconvert-binhex-perl 1.125-3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdata-dump-perl libdata-dump-perl 1.25-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-6+b1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libfcgi-bin libfcgi-bin 2.4.5-0.1 install ok installed libfcgi-perl libfcgi-perl 0.82+ds-3+b2 install ok installed libfcgi0t64:amd64 libfcgi0t64 2.4.5-0.1 install ok installed libffi8:amd64 libffi8 3.4.8-2 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfont-afm-perl libfont-afm-perl 1.20-4 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.3-1 install ok installed libglib2.0-data libglib2.0-data 2.84.3-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-3 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgpm2:amd64 libgpm2 1.20.7-11+b2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhtml-form-perl libhtml-form-perl 6.12-1 install ok installed libhtml-format-perl libhtml-format-perl 2.16-2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.83-1+b2 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.24-1 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-daemon-perl libhttp-daemon-perl 6.16-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 7.00-2 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libio-compress-brotli-perl libio-compress-brotli-perl 0.004001-2+b3 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-sessiondata-perl libio-sessiondata-perl 1.03-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.089-1 install ok installed libio-stringy-perl libio-stringy-perl 2.113-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.14-1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmagic-mgc libmagic-mgc 1:5.46-5 install ok installed libmagic1t64:amd64 libmagic1t64 1:5.46-5 install ok installed libmailtools-perl libmailtools-perl 2.22-1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.4-2 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.4-2 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.4-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmime-tools-perl libmime-tools-perl 5.515-1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libmpfr6:amd64 libmpfr6 4.2.2-1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-smtp-ssl-perl libnet-smtp-ssl-perl 1.04-2 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-3 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-6 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-9 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.5-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.5-2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed libruby:amd64 libruby 1:3.3+b1 install ok installed libruby3.3:amd64 libruby3.3 3.3.8-2 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1+b2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsoap-lite-perl libsoap-lite-perl 1.27-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtask-weaken-perl libtask-weaken-perl 1.06-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.32-1 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed liburi-perl liburi-perl 5.30-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libuv1t64:amd64 libuv1t64 1.50.0-2 install ok installed libwww-perl libwww-perl 6.78-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0207+dfsg+really+2.0134-5+b2 install ok installed libxml-namespacesupport-perl libxml-namespacesupport-perl 1.12-2 install ok installed libxml-parser-perl libxml-parser-perl 2.47-1+b3 install ok installed libxml-sax-base-perl libxml-sax-base-perl 1.09-3 install ok installed libxml-sax-expat-perl libxml-sax-expat-perl 0.51-2 install ok installed libxml-sax-perl libxml-sax-perl 1.02+dfsg-4 install ok installed libxml-simple-perl libxml-simple-perl 2.25-2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-2.1 install ok installed libxmlrpc-lite-perl libxmlrpc-lite-perl 0.717-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed linux-sysctl-defaults linux-sysctl-defaults 4.14 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed lynx lynx 2.9.2-1 install ok installed lynx-common lynx-common 2.9.2-1 install ok installed mafft mafft 7.505-1 install ok installed mailcap mailcap 3.74 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed med-config med-config 3.9.0 install ok installed media-types media-types 13.0.0 install ok installed menu menu 2.1.51 install ok installed mount mount 2.41-5 install ok installed mummer mummer 3.23+dfsg-8 install ok installed muscle muscle 1:5.1.0-1 install ok installed mustang mustang 3.2.4-1 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-7 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-6 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openssl openssl 3.5.1-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl perl 5.40.1-6 install ok installed perl-base perl-base 5.40.1-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-6 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b2 install ok installed poa poa 2.0+20060928-10 install ok installed prank prank 0.0.170427+dfsg-3 install ok installed probcons probcons 1.12-14 install ok installed procps procps 2:4.0.4-9 install ok installed proda proda 1.0-14 install ok installed psmisc psmisc 23.7-2 install ok installed python3 python3 3.13.5-1 install ok installed python3-minimal python3-minimal 3.13.5-1 install ok installed python3.13 python3.13 3.13.5-2 install ok installed python3.13-minimal python3.13-minimal 3.13.5-2 install ok installed rake rake 13.2.1-1 install ok installed readline-common readline-common 8.2-6 install ok installed ruby ruby 1:3.3+b1 install ok installed ruby-bio ruby-bio 2.0.5-1 install ok installed ruby-csv ruby-csv 3.3.4-1 install ok installed ruby-did-you-mean ruby-did-you-mean 1.6.3-2 install ok installed ruby-net-telnet ruby-net-telnet 0.2.0-1 install ok installed ruby-ruby2-keywords ruby-ruby2-keywords 0.0.5-1 install ok installed ruby-rubygems ruby-rubygems 3.6.7-2 install ok installed ruby-sdbm:amd64 ruby-sdbm 1.0.0-5+b7 install ok installed ruby-webrick ruby-webrick 1.9.1-1 install ok installed ruby-xmlrpc ruby-xmlrpc 0.3.3-2 install ok installed ruby3.3 ruby3.3 3.3.8-2 install ok installed rubygems-integration rubygems-integration 1.19 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.25 install ok installed shared-mime-info shared-mime-info 2.4-5+b2 install ok installed sim4 sim4 0.0.20121010-8 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed t-coffee t-coffee 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tm-align tm-align 20190822+dfsg-3 install ok installed tzdata tzdata 2025b-4 install ok installed ucf ucf 3.0052 install ok installed unzip unzip 6.0-29 install ok installed util-linux util-linux 2.41-5 install ok installed xdg-user-dirs xdg-user-dirs 0.18-2 install ok installed xz-utils xz-utils 5.8.1-1 install ok installed zip zip 3.0-15 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-bin', 'libfcgi-perl', 'libfcgi0t64:amd64', 'libffi8:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libidn2-0:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.3:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'libunistring5:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'linux-sysctl-defaults', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'procps', 'proda', 'psmisc', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'rake', 'readline-common', 'ruby', 'ruby-csv', 'ruby-did-you-mean', 'ruby-net-telnet', 'ruby-ruby2-keywords', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.3', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip', 'ruby-bio'] 0m37.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser amap-align blends-common bzip2 ca-certificates clustalo clustalw dialign-tx dialign-tx-data exonerate file fonts-lato fsa gawk hmmer javascript-common kalign libargtable2-0 libatomic1 libauthen-sasl-perl libbrotli1 libclass-inspector-perl libclone-perl libconvert-binhex-perl libdata-dump-perl libdivsufsort3 libencode-locale-perl libexpat1 libfcgi-bin libfcgi-perl libfcgi0t64 libffi8 libfile-listing-perl libfont-afm-perl libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgnutls30t64 libgomp1 libgpm2 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libio-compress-brotli-perl libio-html-perl libio-sessiondata-perl libio-socket-ssl-perl libio-stringy-perl libjs-jquery liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmailtools-perl libmbedcrypto16 libmbedtls21 libmbedx509-7 libmime-tools-perl libmpfr6 libncbi-vdb3 libncursesw6 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnghttp2-14 libp11-kit0 libperl5.40 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libruby libruby3.3 libsigsegv2 libsoap-lite-perl libtask-weaken-perl libtasn1-6 libtext-charwidth-perl libtext-wrapi18n-perl libtimedate-perl libtry-tiny-perl libunistring5 liburi-perl libuv1t64 libwww-perl libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-simple-perl libxml2 libxmlrpc-lite-perl libyaml-0-2 linux-sysctl-defaults lynx lynx-common mafft mailcap med-config media-types menu mummer muscle mustang ncbi-blast+ ncbi-data ncbi-vdb-data netbase openssl perl perl-modules-5.40 perl-openssl-defaults poa prank probcons procps proda psmisc python3 python3-minimal python3.13 python3.13-minimal rake readline-common ruby ruby-bio ruby-csv ruby-did-you-mean ruby-net-telnet ruby-ruby2-keywords ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.3 rubygems-integration sensible-utils shared-mime-info sim4 t-coffee tm-align ucf unzip xdg-user-dirs xz-utils zip 0 upgraded, 0 newly installed, 161 to remove and 0 not upgraded. After this operation, 362 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 ... 16491 files and directories currently installed.) Removing med-config (3.9.0) ... Removing blends-common (0.7.10) ... Removing adduser (3.152) ... Removing amap-align (2.2+git20080214.600fc29+dfsg-2) ... Removing bzip2 (1.0.8-6) ... Removing libxml-simple-perl (2.25-2) ... Removing libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing clustalo (1.2.4-8) ... Removing clustalw (2.1+lgpl-7) ... Removing dialign-tx (1.0.2-15) ... Removing dialign-tx-data (1.0.2-15) ... Removing fsa (1.15.9+dfsg-6) ... Removing exonerate (2.4.0-5+b1) ... Removing file (1:5.46-5) ... Removing fonts-lato (2.015-1) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2+b1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing hmmer (3.4+dfsg-2) ... Removing javascript-common (12+nmu1) ... Removing kalign (1:3.4.0-1+b3) ... Removing libargtable2-0:amd64 (13-4) ... Removing shared-mime-info (2.4-5+b2) ... Removing libglib2.0-0t64:amd64 (2.84.3-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing libauthen-sasl-perl (2.1700-1) ... Removing lynx (2.9.2-1) ... Removing libio-compress-brotli-perl (0.004001-2+b3) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libxmlrpc-lite-perl (0.717-5) ... Removing libsoap-lite-perl (1.27-3) ... Removing libclass-inspector-perl (1.36-3) ... Removing libmime-tools-perl (5.515-1) ... Removing libconvert-binhex-perl (1.125-3) ... Removing libdata-dump-perl (1.25-1) ... Removing libdivsufsort3:amd64 (2.0.1-6+b1) ... Removing ncbi-blast+ (2.16.0+ds-7) ... Removing python3 (3.13.5-1) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13 (3.13.5-2) ... Removing python3.13-minimal (3.13.5-2) ... Removing libfcgi-bin (2.4.5-0.1) ... Removing libfcgi-perl (0.82+ds-3+b2) ... Removing libfcgi0t64:amd64 (2.4.5-0.1) ... Removing ruby-sdbm:amd64 (1.0.0-5+b7) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.5-2) ... Removing libhtml-format-perl (2.16-2) ... Removing libfont-afm-perl (1.20-4) ... Removing mailcap (3.74) ... Removing mafft (7.505-1) ... Removing libhttp-daemon-perl (6.16-1) ... Removing libmailtools-perl (2.22-1) ... Removing libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing libxml-sax-perl (1.02+dfsg-4) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::PurePerl with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Removing tm-align (20190822+dfsg-3) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libglib2.0-data (2.84.3-1) ... Removing libgnutls30t64:amd64 (3.8.9-3) ... Removing muscle (1:5.1.0-1) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgpm2:amd64 (1.20.7-11+b2) ... Removing libhtml-form-perl (6.12-1) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libio-sessiondata-perl (1.03-3) ... Removing libnet-smtp-ssl-perl (1.04-2) ... Removing libio-stringy-perl (2.113-2) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmagic1t64:amd64 (1:5.46-5) ... Removing libmagic-mgc (1:5.46-5) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.4-2) ... Removing libmbedx509-7:amd64 (3.6.4-2) ... Removing libmbedcrypto16:amd64 (3.6.4-2) ... Removing libmpfr6:amd64 (4.2.2-1) ... Removing ucf (3.0052) ... Removing procps (2:4.0.4-9) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libproc2-0:amd64 (2:4.0.4-9) ... Removing libpython3.13-minimal:amd64 (3.13.5-2) ... Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsigsegv2:amd64 (2.14-1+b2) ... Removing libtask-weaken-perl (1.06-2) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libtext-wrapi18n-perl (0.06-10) ... Removing libtext-charwidth-perl:amd64 (0.04-11+b4) ... Removing libunistring5:amd64 (1.3-2) ... Removing libuv1t64:amd64 (1.50.0-2) ... Removing libxml-namespacesupport-perl (1.12-2) ... Removing libxml-sax-base-perl (1.09-3) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Removing linux-sysctl-defaults (4.14) ... Removing lynx-common (2.9.2-1) ... Removing media-types (13.0.0) ... Removing menu (2.1.51) ... Removing mustang (3.2.4-1) ... Removing ncbi-data (6.1.20170106+dfsg2-6) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... Removing poa (2.0+20060928-10) ... Removing prank (0.0.170427+dfsg-3) ... Removing probcons (1.12-14) ... Removing proda (1.0-14) ... Removing psmisc (23.7-2) ... Removing readline-common (8.2-6) ... Removing ruby-bio (2.0.5-1) ... Removing sensible-utils (0.0.25) ... Removing sim4 (0.0.20121010-8) ... Removing t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... Removing unzip (6.0-29) ... Removing xdg-user-dirs (0.18-2) ... Removing xz-utils (5.8.1-1) ... Removing zip (3.0-15) ... Removing libxml-parser-perl (2.47-1+b3) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libruby3.3:amd64 (3.3.8-2) ... Removing rake (13.2.1-1) ... Removing ruby (1:3.3+b1) ... Removing ruby-rubygems (3.6.7-2) ... Removing libwww-perl (6.78-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libffi8:amd64 (3.4.8-2) ... Removing libfile-listing-perl (6.16-1) ... Removing libhttp-cookies-perl (6.11-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing liblwp-protocol-https-perl (6.14-1) ... Removing libnet-http-perl (6.23-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.83-1+b2) ... Removing libhtml-tagset-perl (3.24-1) ... Removing libio-socket-ssl-perl (2.089-1) ... Removing libnet-ssleay-perl:amd64 (1.94-3) ... Removing libruby:amd64 (1:3.3+b1) ... Removing libtry-tiny-perl (0.32-1) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing netbase (6.5) ... Removing perl-openssl-defaults:amd64 (7+b2) ... Removing ruby-csv (3.3.4-1) ... Removing ruby-did-you-mean (1.6.3-2) ... Removing ruby-net-telnet (0.2.0-1) ... Removing ruby-ruby2-keywords (0.0.5-1) ... Removing ruby-xmlrpc (0.3.3-2) ... Removing ruby-webrick (1.9.1-1) ... Removing ruby3.3 (3.3.8-2) ... Removing rubygems-integration (1.19) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (7.00-2) ... Removing libclone-perl:amd64 (0.47-1+b1) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.06-1) ... Removing liburi-perl (5.30-1) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing libtimedate-perl (2.3300-2) ... Removing openssl (3.5.1-1) ... Removing perl (5.40.1-6) ... Removing libperl5.40:amd64 (5.40.1-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing perl-modules-5.40 (5.40.1-6) ... Processing triggers for libc-bin (2.41-12) ... 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-bin', 'libfcgi-perl', 'libfcgi0t64:amd64', 'libffi8:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libidn2-0:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.3:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'libunistring5:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'linux-sysctl-defaults', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+-', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'procps', 'proda', 'psmisc', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'rake', 'readline-common', 'ruby', 'ruby-csv', 'ruby-did-you-mean', 'ruby-net-telnet', 'ruby-ruby2-keywords', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.3', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip', 'ruby-bio'] 0m37.5s INFO: Running scripts post_remove 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_remove_exceptions'] 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_remove_exceptions'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-bin', 'libfcgi-perl', 'libfcgi0t64:amd64', 'libffi8:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libidn2-0:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.3:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'libunistring5:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'linux-sysctl-defaults', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'procps', 'proda', 'psmisc', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'rake', 'readline-common', 'ruby', 'ruby-csv', 'ruby-did-you-mean', 'ruby-net-telnet', 'ruby-ruby2-keywords', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.3', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip'] 0m37.9s DUMP: (Reading database ... 4994 files and directories currently installed.) Purging configuration files for adduser (3.152) ... dpkg: warning: ignoring request to remove amap-align which isn't installed Purging configuration files for blends-common (0.7.10) ... dpkg: warning: ignoring request to remove bzip2 which isn't installed Purging configuration files for ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove clustalo which isn't installed Purging configuration files for clustalw (2.1+lgpl-7) ... dpkg: warning: ignoring request to remove dialign-tx which isn't installed dpkg: warning: ignoring request to remove dialign-tx-data which isn't installed dpkg: warning: ignoring request to remove exonerate which isn't installed dpkg: warning: ignoring request to remove file which isn't installed dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fsa which isn't installed Purging configuration files for gawk (1:5.2.1-2+b1) ... dpkg: warning: ignoring request to remove hmmer which isn't installed Purging configuration files for javascript-common (12+nmu1) ... dpkg: warning: ignoring request to remove kalign which isn't installed dpkg: warning: ignoring request to remove libargtable2-0 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libauthen-sasl-perl which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libclass-inspector-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libconvert-binhex-perl which isn't installed dpkg: warning: ignoring request to remove libdata-dump-perl which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfcgi-bin which isn't installed dpkg: warning: ignoring request to remove libfcgi-perl which isn't installed dpkg: warning: ignoring request to remove libfcgi0t64 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfont-afm-perl which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.84.3-1) ... dpkg: warning: ignoring request to remove libglib2.0-data which isn't installed dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpm2 which isn't installed dpkg: warning: ignoring request to remove libhtml-form-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-format-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-daemon-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libio-compress-brotli-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-sessiondata-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-stringy-perl which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1t64:amd64 (1:5.46-5) ... dpkg: warning: ignoring request to remove libmailtools-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libmime-tools-perl which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-smtp-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.5-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove libruby which isn't installed dpkg: warning: ignoring request to remove libruby3.3 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsoap-lite-perl which isn't installed dpkg: warning: ignoring request to remove libtask-weaken-perl which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtext-charwidth-perl which isn't installed dpkg: warning: ignoring request to remove libtext-wrapi18n-perl which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libxml-libxml-perl which isn't installed dpkg: warning: ignoring request to remove libxml-namespacesupport-perl which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-base-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-expat-perl which isn't installed Purging configuration files for libxml-sax-perl (1.02+dfsg-4) ... dpkg: warning: ignoring request to remove libxml-simple-perl which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmlrpc-lite-perl which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove linux-sysctl-defaults which isn't installed Purging configuration files for lynx (2.9.2-1) ... Purging configuration files for lynx-common (2.9.2-1) ... dpkg: warning: ignoring request to remove mafft which isn't installed Purging configuration files for mailcap (3.74) ... Purging configuration files for med-config (3.9.0) ... Purging configuration files for media-types (13.0.0) ... Purging configuration files for menu (2.1.51) ... dpkg: warning: ignoring request to remove mummer which isn't installed dpkg: warning: ignoring request to remove muscle which isn't installed dpkg: warning: ignoring request to remove mustang which isn't installed dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-6) ... Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... Purging configuration files for netbase (6.5) ... Purging configuration files for openssl (3.5.1-1) ... Purging configuration files for perl (5.40.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove poa which isn't installed dpkg: warning: ignoring request to remove prank which isn't installed dpkg: warning: ignoring request to remove probcons which isn't installed Purging configuration files for procps (2:4.0.4-9) ... dpkg: warning: ignoring request to remove proda which isn't installed dpkg: warning: ignoring request to remove psmisc which isn't installed Purging configuration files for python3 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.5-2) ... dpkg: warning: ignoring request to remove rake which isn't installed Purging configuration files for readline-common (8.2-6) ... dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove ruby-csv which isn't installed dpkg: warning: ignoring request to remove ruby-did-you-mean which isn't installed dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby-ruby2-keywords which isn't installed dpkg: warning: ignoring request to remove ruby-rubygems which isn't installed dpkg: warning: ignoring request to remove ruby-sdbm which isn't installed dpkg: warning: ignoring request to remove ruby-webrick which isn't installed dpkg: warning: ignoring request to remove ruby-xmlrpc which isn't installed dpkg: warning: ignoring request to remove ruby3.3 which isn't installed dpkg: warning: ignoring request to remove rubygems-integration which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for shared-mime-info (2.4-5+b2) ... dpkg: warning: ignoring request to remove sim4 which isn't installed dpkg: warning: ignoring request to remove t-coffee which isn't installed dpkg: warning: ignoring request to remove tm-align which isn't installed Purging configuration files for ucf (3.0052) ... dpkg: warning: ignoring request to remove unzip which isn't installed Purging configuration files for xdg-user-dirs (0.18-2) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', 'adduser', 'amap-align', 'blends-common', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dialign-tx', 'dialign-tx-data', 'exonerate', 'file', 'fonts-lato', 'fsa', 'gawk', 'hmmer', 'javascript-common', 'kalign', 'libargtable2-0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libbrotli1:amd64', 'libclass-inspector-perl', 'libclone-perl:amd64', 'libconvert-binhex-perl', 'libdata-dump-perl', 'libdivsufsort3:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfcgi-bin', 'libfcgi-perl', 'libfcgi0t64:amd64', 'libffi8:amd64', 'libfile-listing-perl', 'libfont-afm-perl', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libidn2-0:amd64', 'libio-compress-brotli-perl', 'libio-html-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-stringy-perl', 'libjs-jquery', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmailtools-perl', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmime-tools-perl', 'libmpfr6:amd64', 'libncbi-vdb3:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libperl5.40:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'libruby:amd64', 'libruby3.3:amd64', 'libsigsegv2:amd64', 'libsoap-lite-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtext-charwidth-perl:amd64', 'libtext-wrapi18n-perl', 'libtimedate-perl', 'libtry-tiny-perl', 'libunistring5:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libxml-libxml-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-simple-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libyaml-0-2:amd64', 'linux-sysctl-defaults', 'lynx', 'lynx-common', 'mafft', 'mailcap', 'med-config', 'media-types', 'menu', 'mummer', 'muscle', 'mustang', 'ncbi-blast+', 'ncbi-data', 'ncbi-vdb-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'perl-openssl-defaults:amd64', 'poa', 'prank', 'probcons', 'procps', 'proda', 'psmisc', 'python3', 'python3-minimal', 'python3.13', 'python3.13-minimal', 'rake', 'readline-common', 'ruby', 'ruby-csv', 'ruby-did-you-mean', 'ruby-net-telnet', 'ruby-ruby2-keywords', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.3', 'rubygems-integration', 'sensible-utils', 'shared-mime-info', 'sim4', 't-coffee', 'tm-align', 'ucf', 'unzip', 'xdg-user-dirs', 'xz-utils', 'zip'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', 'ruby-bio'] 0m37.9s DUMP: dpkg: warning: ignoring request to remove ruby-bio which isn't installed 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', 'ruby-bio'] 0m37.9s INFO: Running scripts post_purge 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_purge_exceptions'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_purge_exceptions'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', '--pending'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--purge', '--pending'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--remove', '--pending'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg', '--remove', '--pending'] 0m38.0s INFO: Running scripts post_test 0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_test_exceptions'] 0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'tmp/scripts/post_test_exceptions'] 0m38.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m38.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m38.6s DEBUG: No broken symlinks as far as we can find. 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-divert', '--list'] 0m38.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'dpkg-divert', '--list'] 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'clean'] 0m38.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphu546fwf', 'apt-get', 'clean'] 0m38.7s DEBUG: Recording chroot state 0m39.2s INFO: PASS: Installation and purging test. 0m39.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/shm'] 0m39.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/shm'] 0m39.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/console'] 0m39.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/console'] 0m39.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/ptmx'] 0m39.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/ptmx'] 0m39.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts'] 0m39.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/dev/pts'] 0m39.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/proc'] 0m39.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphu546fwf/proc'] 0m39.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m39.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphu546fwf'] 0m39.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmphu546fwf 0m39.8s INFO: PASS: All tests. 0m39.8s INFO: piuparts run ends. ret=0 End: 2025-08-17 01:01:34 GMT