Start: 2024-12-23 09:10:45 GMT Package: hisat2 Source: hisat2 (2.2.1-5) Version: 2.2.1-5+b1 Installed-Size: 14675 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Description: graph-based alignment of short nucleotide reads to many genomes Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.8.2-2) Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-5+b1_amd64.deb Size: 3805940 MD5sum: 306cd16cce064210ba1f6f225a366796 SHA256: 98b73a974241176bda5650dd777412510b91ea424d3b1e6dafc01a90a8965228 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt hisat2=2.2.1-5+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt hisat2=2.2.1-5+b1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpv657eaz2 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpv657eaz2 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/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/tmpv657eaz2/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpv657eaz2/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'update'] 0m3.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9387 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6296 kB] Fetched 15.9 MB in 2s (7988 kB/s) Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', '-yf', 'dist-upgrade'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s DUMP: 5562c5d072eec84714f061a3b931a3a9 - 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s INFO: Running scripts post_setup 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_dummy_users'] 0m5.6s 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 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_dummy_users'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s 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' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'clean'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'clean'] 0m5.6s DEBUG: Recording chroot state 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.3s DUMP: install ok installed apt apt 2.9.17 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.17 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 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 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257-2 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-divert', '--list'] 0m6.3s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 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 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-divert', '--list'] 0m6.3s INFO: Running scripts is_testable 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s INFO: apt-cache does not know about any of the requested packages 0m6.3s INFO: Running scripts pre_test 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_test_root_password'] 0m6.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_test_root_password'] 0m6.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 0m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 0m7.2s DEBUG: No broken symlinks as far as we can find. 0m7.2s INFO: Running scripts pre_install 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 0m7.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 0m8.4s DEBUG: No broken symlinks as far as we can find. 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-cache', 'policy'] 0m9.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-cache', 'policy'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-cache', 'policy', 'hisat2'] 0m9.6s DUMP: hisat2: Installed: (none) Candidate: 2.2.1-5+b1 Version table: 2.2.1-5+b1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-cache', 'policy', 'hisat2'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', '-y', 'install', 'hisat2=2.2.1-5+b1'] 1m56.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bcftools binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu isympy-common isympy3 javascript-common krb5-locales libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 libldap-common liblerc4 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsframe1 libsharpyuv0 libsqlite3-0 libssh2-1t64 libstdc++-14-dev libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 publicsuffix python-biopython-doc python-matplotlib-data python3 python3-argcomplete python3-argh python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cssselect python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-gffutils python3-hisat2 python3-html5lib python3-idna python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-olefile python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pooch python3-pybedtools python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-simplejson python3-soupsieve python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto samtools sgml-base shared-mime-info tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core Suggested packages: texlive-latex-recommended binutils-doc gprofng-gui blt-demo cpp-doc gcc-14-locales cpp-14-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib g++-14-multilib gcc-14-doc gcc-multilib make autoconf automake libtool flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu apache2 | lighttpd | httpd libc-devtools glibc-doc gdbm-l10n low-memory-monitor gpm krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils sensible-utils libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql libstdc++-14-doc tcl8.6 tk8.6 man-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise python-charset-normalizer-doc python-cycler-doc python3-genshi python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools python3-paramiko python-pybedtools-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.12-venv python3.12-doc binfmt-support readline-doc cwltool sgml-base-doc debhelper Recommended packages: python3-biopython The following NEW packages will be installed: bcftools binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu hisat2 isympy-common isympy3 javascript-common krb5-locales libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 libldap-common liblerc4 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsframe1 libsharpyuv0 libsqlite3-0 libssh2-1t64 libstdc++-14-dev libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 publicsuffix python-biopython-doc python-matplotlib-data python3 python3-argcomplete python3-argh python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cssselect python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-gffutils python3-hisat2 python3-html5lib python3-idna python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-olefile python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pooch python3-pybedtools python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-simplejson python3-soupsieve python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto samtools sgml-base shared-mime-info tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core 0 upgraded, 237 newly installed, 0 to remove and 0 not upgraded. Need to get 256 MB of archives. After this operation, 1042 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:11 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 krb5-locales all 1.21.3-3 [101 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 manpages all 6.9.1-1 [1393 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.20-2 [760 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 binutils-common amd64 2.43.50.20241215-1 [2630 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libsframe1 amd64 2.43.50.20241215-1 [77.5 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libbinutils amd64 2.43.50.20241215-1 [533 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libctf-nobfd0 amd64 2.43.50.20241215-1 [155 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libctf0 amd64 2.43.50.20241215-1 [88.6 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libgprofng0 amd64 2.43.50.20241215-1 [809 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 binutils-x86-64-linux-gnu amd64 2.43.50.20241215-1 [2275 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 binutils amd64 2.43.50.20241215-1 [68.3 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:68 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:82 http://deb.debian.org/debian trixie/main amd64 libisl23 amd64 0.27-1 [659 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8 [11.1 MB] Get:86 http://deb.debian.org/debian trixie/main amd64 cpp-14 amd64 14.2.0-8 [1276 B] Get:87 http://deb.debian.org/debian trixie/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Get:88 http://deb.debian.org/debian trixie/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Get:89 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libcc1-0 amd64 14.2.0-8 [42.8 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:95 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8 [21.4 MB] Get:103 http://deb.debian.org/debian trixie/main amd64 gcc-14 amd64 14.2.0-8 [530 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Get:105 http://deb.debian.org/debian trixie/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Get:106 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-4 [52.0 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.12.5-1 [2474 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-4 [1954 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8 [12.1 MB] Get:113 http://deb.debian.org/debian trixie/main amd64 g++-14 amd64 14.2.0-8 [20.2 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Get:115 http://deb.debian.org/debian trixie/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Get:116 http://deb.debian.org/debian trixie/main amd64 hisat2 amd64 2.2.1-5+b1 [3806 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 isympy-common all 1.13.3-1 [234 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 isympy3 all 1.13.3-1 [6296 B] Get:121 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:122 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libglib2.0-data all 2.82.4-1 [1276 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libgpm2 amd64 1.20.7-11+b1 [14.4 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libldap-common all 2.5.18+dfsg-3 [32.0 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules amd64 2.1.28+dfsg1-8 [66.5 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 manpages-dev all 6.9.1-1 [2122 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Get:167 http://deb.debian.org/debian trixie/main amd64 publicsuffix all 20241025.1547-0.1 [287 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 python-biopython-doc all 1.84+dfsg-4 [18.2 MB] Get:169 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 python3-argcomplete all 3.5.2-1 [40.2 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 python3-argh all 0.31.3-1 [26.6 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:181 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.8-3 [113 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.1-2 [103 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get:188 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:193 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4+b1 [1651 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 python3-bs4 all 4.12.3-3 [133 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:201 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 python3-cssselect all 1.2.0-4 [21.7 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:205 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-5.1 [95.2 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB] Get:213 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.55.0-3 [1634 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.3-1 [29.1 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 python3-simplejson amd64 3.19.3-1+b1 [61.8 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 python3-gffutils all 0.13-1 [1041 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 python3-hisat2 all 2.2.1-5 [14.0 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 python3-html5lib all 1.2-1 [92.2 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 python3-olefile all 0.47-1 [39.3 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.2.3-4 [112 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 python3-pooch all 1.8.2-1 [58.4 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 python3-pybedtools amd64 0.10.0-2 [12.3 MB] Get:234 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-1 [91.0 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 xdg-user-dirs amd64 0.18-1 [54.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 256 MB in 2s (149 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 5135 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (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 ... 5455 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding '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' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding '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' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... 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Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libgpm2:amd64 (1.20.7-11+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up xdg-user-dirs (0.18-1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up manpages (6.9.1-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.2.1-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libsasl2-modules:amd64 (2.1.28+dfsg1-8) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up binutils-common:amd64 (2.43.50.20241215-1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up linux-libc-dev (6.12.5-1) ... Setting up libctf-nobfd0:amd64 (2.43.50.20241215-1) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up krb5-locales (1.21.3-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libldap-common (2.5.18+dfsg-3) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libsframe1:amd64 (2.43.50.20241215-1) ... Setting up libjansson4:amd64 (2.14-2+b3) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libglib2.0-data (2.82.4-1) ... Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libmpfr6:amd64 (4.2.1-1+b2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libquadmath0:amd64 (14.2.0-8) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-3) ... Setting up libmpc3:amd64 (1.3.1-1+b3) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libubsan1:amd64 (14.2.0-8) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up libhwasan0:amd64 (14.2.0-8) ... Setting up libcrypt-dev:amd64 (1:4.4.36-5) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libasan8:amd64 (14.2.0-8) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libmbedcrypto16:amd64 (3.6.2-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtsan2:amd64 (14.2.0-8) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.43.50.20241215-1) ... Setting up libisl23:amd64 (0.27-1) ... Setting up libc-dev-bin (2.40-4) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-6) ... Setting up publicsuffix (20241025.1547-0.1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libcc1-0:amd64 (14.2.0-8) ... Setting up liblsan0:amd64 (14.2.0-8) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libitm1:amd64 (14.2.0-8) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libctf0:amd64 (2.43.50.20241215-1) ... Setting up manpages-dev (6.9.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libglib2.0-0t64:amd64 (2.82.4-1) ... No schema files found: doing nothing. Setting up libgprofng0:amd64 (2.43.50.20241215-1) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up shared-mime-info (2.4-5+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-8) ... Setting up libjs-sphinxdoc (8.1.3-2) ... Setting up cpp-14 (14.2.0-8) ... Setting up libmbedtls21:amd64 (3.6.2-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up python-biopython-doc (1.84+dfsg-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libc6-dev:amd64 (2.40-4) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libgcc-14-dev:amd64 (14.2.0-8) ... Setting up libstdc++-14-dev:amd64 (14.2.0-8) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up binutils-x86-64-linux-gnu (2.43.50.20241215-1) ... Setting up cpp-x86-64-linux-gnu (4:14.2.0-1) ... Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up python3.12-tk (3.12.8-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up binutils (2.43.50.20241215-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up cpp (4:14.2.0-1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-8) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up gcc-x86-64-linux-gnu (4:14.2.0-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.8-3) ... Setting up bcftools (1.20-2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up gcc-14 (14.2.0-8) ... Setting up samtools (1.20-3) ... Setting up g++-14-x86-64-linux-gnu (14.2.0-8) ... Setting up g++-x86-64-linux-gnu (4:14.2.0-1) ... Setting up g++-14 (14.2.0-8) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.2-1) ... Setting up gcc (4:14.2.0-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-simplejson (3.19.3-1+b1) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-html5lib (1.2-1) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up g++ (4:14.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up hisat2 (2.2.1-5+b1) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-argcomplete (3.5.2-1) ... Setting up python3-cssselect (1.2.0-4) ... Setting up python3-soupsieve (2.6-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-argh (0.31.3-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-hisat2 (2.2.1-5) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up python3-olefile (0.47-1) ... Setting up python3-tqdm (4.67.1-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up isympy-common (1.13.3-1) ... Setting up python3-tk:amd64 (3.12.7-1) ... Setting up python3-bs4 (4.12.3-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up isympy3 (1.13.3-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-pyfaidx (0.8.1.3-1) ... Setting up python3-fs (2.4.16-5.1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-contourpy (1.3.1-1) ... Setting up python3-pybedtools (0.10.0-2) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pooch (1.8.2-1) ... Setting up python3-fonttools (4.55.0-3) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... Setting up python3-gffutils (0.13-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', '-y', 'install', 'hisat2=2.2.1-5+b1'] 1m56.2s INFO: Running scripts post_install 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_install_exceptions'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_install_exceptions'] 1m56.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 1m58.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 2m2.2s DEBUG: No broken symlinks as far as we can find. 2m4.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', '-ac', '--ignore-obsolete'] 2m8.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', '-ac', '--ignore-obsolete'] 2m8.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m8.8s DUMP: 0.15.6 2m8.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m8.8s INFO: Running adequate version 0.15.6 now. 2m8.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'hisat2'] 2m9.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'hisat2'] 2m9.0s INFO: Running scripts pre_remove 2m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_exceptions'] 2m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/pre_remove_exceptions'] 2m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m13.5s DUMP: install ok installed apt apt 2.9.17 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bcftools bcftools 1.20-2 install ok installed binutils binutils 2.43.50.20241215-1 install ok installed binutils-common:amd64 binutils-common 2.43.50.20241215-1 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.43.50.20241215-1 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed cpp cpp 4:14.2.0-1 install ok installed cpp-14 cpp-14 14.2.0-8 install ok installed cpp-14-x86-64-linux-gnu cpp-14-x86-64-linux-gnu 14.2.0-8 install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:14.2.0-1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed g++ g++ 4:14.2.0-1 install ok installed g++-14 g++-14 14.2.0-8 install ok installed g++-14-x86-64-linux-gnu g++-14-x86-64-linux-gnu 14.2.0-8 install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:14.2.0-1 install ok installed gcc gcc 4:14.2.0-1 install ok installed gcc-14 gcc-14 14.2.0-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu 14.2.0-8 install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:14.2.0-1 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hisat2 hisat2 2.2.1-5+b1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed isympy-common isympy-common 1.13.3-1 install ok installed isympy3 isympy3 1.13.3-1 install ok installed javascript-common javascript-common 11+nmu1 install ok installed krb5-locales krb5-locales 1.21.3-3 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.17 install ok installed libasan8:amd64 libasan8 14.2.0-8 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libbinutils:amd64 libbinutils 2.43.50.20241215-1 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 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 2.40-4 install ok installed libc-dev-bin libc-dev-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libc6-dev:amd64 libc6-dev 2.40-4 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcc1-0:amd64 libcc1-0 14.2.0-8 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.43.50.20241215-1 install ok installed libctf0:amd64 libctf0 2.43.50.20241215-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-8 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 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 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.4-1 install ok installed libglib2.0-data libglib2.0-data 2.82.4-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libgpm2:amd64 libgpm2 1.20.7-11+b1 install ok installed libgprofng0:amd64 libgprofng0 2.43.50.20241215-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.1.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-8 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libisl23:amd64 libisl23 0.27-1 install ok installed libitm1:amd64 libitm1 14.2.0-8 install ok installed libjansson4:amd64 libjansson4 2.14-2+b3 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 8.1.3-2 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-4 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed libldap-common libldap-common 2.5.18+dfsg-3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b2 install ok installed liblsan0:amd64 liblsan0 14.2.0-8 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b3 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b2 install ok installed libncurses6:amd64 libncurses6 6.5-2+b1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.6.0-2 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.9.1-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.9.1-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-3 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.8-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.8-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-8 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules:amd64 libsasl2-modules 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsframe1:amd64 libsframe1 2.43.50.20241215-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-8 install ok installed libubsan1:amd64 libubsan1 14.2.0-8 install ok installed libudev1:amd64 libudev1 257-2 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b3 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b3 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed linux-libc-dev linux-libc-dev 6.12.5-1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed manpages manpages 6.9.1-1 install ok installed manpages-dev manpages-dev 6.9.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-12 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-5 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed publicsuffix publicsuffix 20241025.1547-0.1 install ok installed python-biopython-doc python-biopython-doc 1.84+dfsg-4 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.12.7-1 install ok installed python3-argcomplete python3-argcomplete 3.5.2-1 install ok installed python3-argh python3-argh 0.31.3-1 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-biopython python3-biopython 1.84+dfsg-4+b1 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-bs4 python3-bs4 4.12.3-3 install ok installed python3-cairo python3-cairo 1.26.1-2+b1 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1+b1 install ok installed python3-contourpy python3-contourpy 1.3.1-1 install ok installed python3-cssselect python3-cssselect 1.2.0-4 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-fonttools python3-fonttools 4.55.0-3 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-fs python3-fs 2.4.16-5.1 install ok installed python3-gffutils python3-gffutils 0.13-1 install ok installed python3-hisat2 python3-hisat2 2.2.1-5 install ok installed python3-html5lib python3-html5lib 1.2-1 install ok installed python3-idna python3-idna 3.8-2 install ok installed python3-importlib-metadata python3-importlib-metadata 8.5.0-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-2+b1 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1+b1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-12 install ok installed python3-olefile python3-olefile 0.47-1 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 75.6.0-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-pooch python3-pooch 1.8.2-1 install ok installed python3-pybedtools python3-pybedtools 0.10.0-2 install ok installed python3-pyfaidx python3-pyfaidx 0.8.1.3-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b2 install ok installed python3-reportlab python3-reportlab 4.2.5-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.14.1-3 install ok installed python3-simplejson python3-simplejson 3.19.3-1+b1 install ok installed python3-soupsieve python3-soupsieve 2.6-1 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-tk:amd64 python3-tk 3.12.7-1 install ok installed python3-tqdm python3-tqdm 4.67.1-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.2-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-urllib3 python3-urllib3 2.2.3-4 install ok installed python3-webencodings python3-webencodings 0.5.1-5 install ok installed python3-zipp python3-zipp 3.21.0-1 install ok installed python3.12 python3.12 3.12.8-3 install ok installed python3.12-minimal python3.12-minimal 3.12.8-3 install ok installed python3.12-tk python3.12-tk 3.12.8-3 install ok installed python3.13-tk python3.13-tk 3.13.1-2 install ok installed readline-common readline-common 8.2-6 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed shared-mime-info shared-mime-info 2.4-5+b1 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024b-4 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-user-dirs xdg-user-dirs 0.18-1 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 2m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'remove', 'bcftools', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'isympy-common', 'isympy3', 'javascript-common', 'krb5-locales', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libldap-common', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'publicsuffix', 'python-biopython-doc', 'python-matplotlib-data', 'python3', 'python3-argcomplete', 'python3-argh', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cssselect', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gffutils', 'python3-hisat2', 'python3-html5lib', 'python3-idna', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-olefile', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pooch', 'python3-pybedtools', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-simplejson', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-webencodings', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'samtools', 'sgml-base', 'shared-mime-info', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'hisat2'] 3m3.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bcftools binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu hisat2 isympy-common isympy3 javascript-common krb5-locales libasan8 libatomic1 libbinutils libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libglib2.0-data libgomp1 libgpm2 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 libldap-common liblerc4 liblmdb0 liblsan0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsframe1 libsharpyuv0 libsqlite3-0 libssh2-1t64 libstdc++-14-dev libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 linux-libc-dev manpages manpages-dev media-types ncbi-blast+ ncbi-data netbase openssl perl perl-modules-5.40 publicsuffix python-biopython-doc python-matplotlib-data python3 python3-argcomplete python3-argh python3-attr python3-autocommand python3-biopython python3-brotli python3-bs4 python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cssselect python3-cycler python3-dateutil python3-decorator python3-fonttools python3-freetype python3-fs python3-gffutils python3-hisat2 python3-html5lib python3-idna python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-olefile python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-platformdirs python3-pooch python3-pybedtools python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-simplejson python3-soupsieve python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-webencodings python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto samtools sgml-base shared-mime-info tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xdg-user-dirs xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 237 to remove and 0 not upgraded. After this operation, 1042 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 ... 31051 files and directories currently installed.) Removing bcftools (1.20-2) ... Removing g++ (4:14.2.0-1) ... Removing gcc (4:14.2.0-1) ... Removing g++-x86-64-linux-gnu (4:14.2.0-1) ... Removing gcc-x86-64-linux-gnu (4:14.2.0-1) ... Removing g++-14 (14.2.0-8) ... Removing g++-14-x86-64-linux-gnu (14.2.0-8) ... Removing python3-gffutils (0.13-1) ... Removing python3-biopython (1.84+dfsg-4+b1) ... Removing python3-reportlab (4.2.5-1) ... Removing python3-matplotlib (3.8.3-3+b1) ... Removing python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Removing python3-pil:amd64 (10.4.0-1+b1) ... Removing python3-tk:amd64 (3.12.7-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-pooch (1.8.2-1) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:14.2.0-1) ... Removing cpp-x86-64-linux-gnu (4:14.2.0-1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.1-2) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.1-2+b1) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.2.1-1) ... Removing python3-hisat2 (2.2.1-5) ... Removing hisat2 (2.2.1-5+b1) ... Removing isympy3 (1.13.3-1) ... Removing isympy-common (1.13.3-1) ... Removing javascript-common (11+nmu1) ... Removing krb5-locales (1.21.3-3) ... Removing libstdc++-14-dev:amd64 (14.2.0-8) ... Removing shared-mime-info (2.4-5+b1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.1.0-1) ... Removing libglib2.0-0t64:amd64 (2.82.4-1) ... Removing python3-pybedtools (0.10.0-2) ... Removing python3-contourpy (1.3.1-1) ... Removing python3-freetype (2.5.1-1) ... Removing samtools (1.20-3) ... Removing libc6-dev:amd64 (2.40-4) ... Removing libc-dev-bin (2.40-4) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing python3-simplejson (3.19.3-1+b1) ... Removing python3-tqdm (4.67.1-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-pyfaidx (0.8.1.3-1) ... Removing python3-importlib-metadata (8.5.0-1) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing ncbi-blast+ (2.16.0+ds-6+b1) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libglib2.0-data (2.82.4-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgpm2:amd64 (1.20.7-11+b1) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing python-biopython-doc (1.84+dfsg-4) ... Removing libjs-sphinxdoc (8.1.3-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap-common (2.5.18+dfsg-3) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing liblmdb0:amd64 (0.9.31-1+b2) ... Removing libmbedtls21:amd64 (3.6.2-3) ... Removing libmbedx509-7:amd64 (3.6.2-3) ... Removing libmbedcrypto16:amd64 (3.6.2-3) ... Removing libncurses6:amd64 (6.5-2+b1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libsasl2-modules:amd64 (2.1.28+dfsg1-8) ... Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing python3.12-tk (3.12.8-3) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing linux-libc-dev (6.12.5-1) ... Removing manpages-dev (6.9.1-1) ... Removing manpages (6.9.1-1) ... Removing ncbi-data (6.1.20170106+dfsg2-5) ... Removing openssl (3.3.2-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing publicsuffix (20241025.1547-0.1) ... Removing python3-argcomplete (3.5.2-1) ... Removing python3-argh (0.31.3-1) ... Removing python3-bs4 (4.12.3-3) ... Removing python3-charset-normalizer (3.4.0-1+b1) ... Removing python3-cssselect (1.2.0-4) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-html5lib (1.2-1) ... Removing python3-idna (3.8-2) ... Removing python3-kiwisolver (1.4.7-2+b1) ... Removing python3-olefile (0.47-1) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-pysam (0.22.1+ds-2+b2) ... Removing python3-soupsieve (2.6-1) ... Removing python3-urllib3 (2.2.3-4) ... Removing python3-webencodings (0.5.1-5) ... Removing python3-zipp (3.21.0-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xdg-user-dirs (0.18-1) ... Removing gcc-14 (14.2.0-8) ... Removing binutils (2.43.50.20241215-1) ... Removing gcc-14-x86-64-linux-gnu (14.2.0-8) ... Removing binutils-x86-64-linux-gnu (2.43.50.20241215-1) ... Removing libgprofng0:amd64 (2.43.50.20241215-1) ... Removing libctf0:amd64 (2.43.50.20241215-1) ... Removing libbinutils:amd64 (2.43.50.20241215-1) ... Removing binutils-common:amd64 (2.43.50.20241215-1) ... Removing cpp-14 (14.2.0-8) ... Removing cpp-14-x86-64-linux-gnu (14.2.0-8) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b3) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-urw-base35 (20200910-8) ... Removing libgcc-14-dev:amd64 (14.2.0-8) ... Removing libasan8:amd64 (14.2.0-8) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing xfonts-utils (1:7.7+7) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.11.1-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libcc1-0:amd64 (14.2.0-8) ... Removing libctf-nobfd0:amd64 (2.43.50.20241215-1) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libfontenc1:amd64 (1:1.1.8-1+b1) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libhwasan0:amd64 (14.2.0-8) ... Removing libisl23:amd64 (0.27-1) ... Removing libitm1:amd64 (14.2.0-8) ... Removing libjansson4:amd64 (2.14-2+b3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblsan0:amd64 (14.2.0-8) ... Removing libmpc3:amd64 (1.3.1-1+b3) ... Removing libmpfr6:amd64 (4.2.1-1+b2) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.6.0-2) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Removing libngtcp2-16:amd64 (1.9.1-1) ... Removing libpng16-16t64:amd64 (1.6.44-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libquadmath0:amd64 (14.2.0-8) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libsframe1:amd64 (2.43.50.20241215-1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libtsan2:amd64 (14.2.0-8) ... Removing libubsan1:amd64 (14.2.0-8) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b3) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-ufolib2 (0.17.0+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3-fonttools (4.55.0-3) ... Removing python3-scipy (1.14.1-3) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing python3-fs (2.4.16-5.1) ... Removing python3-pkg-resources (75.6.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-sympy (1.13.3-1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing python3-lxml:amd64 (5.3.0-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-lz4 (4.4.0+dfsg-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-tz (2024.2-1) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.8-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.8-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.8-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.8-3) ... find: '/usr/lib/python3': No such file or directory 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 libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.40-4) ... 3m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'remove', 'bcftools', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'isympy-common', 'isympy3', 'javascript-common', 'krb5-locales', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libldap-common', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'publicsuffix', 'python-biopython-doc', 'python-matplotlib-data', 'python3', 'python3-argcomplete', 'python3-argh', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cssselect', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gffutils', 'python3-hisat2', 'python3-html5lib', 'python3-idna', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-olefile', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pooch', 'python3-pybedtools', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-simplejson', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-webencodings', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'samtools', 'sgml-base', 'shared-mime-info', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'hisat2'] 3m3.9s INFO: Running scripts post_remove 3m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_remove_exceptions'] 3m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_remove_exceptions'] 3m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', 'bcftools', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'isympy-common', 'isympy3', 'javascript-common', 'krb5-locales', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libldap-common', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'publicsuffix', 'python-biopython-doc', 'python-matplotlib-data', 'python3', 'python3-argcomplete', 'python3-argh', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cssselect', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gffutils', 'python3-hisat2', 'python3-html5lib', 'python3-idna', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-olefile', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pooch', 'python3-pybedtools', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-simplejson', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-webencodings', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'samtools', 'sgml-base', 'shared-mime-info', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m4.7s DUMP: dpkg: warning: ignoring request to remove bcftools which isn't installed dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 5220 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.43.50.20241215-1) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for cpp (4:14.2.0-1) ... dpkg: warning: ignoring request to remove cpp-14 which isn't installed dpkg: warning: ignoring request to remove cpp-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove cpp-x86-64-linux-gnu which isn't installed Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... dpkg: warning: ignoring request to remove fonts-dejavu-extra which isn't installed Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-14 which isn't installed dpkg: warning: ignoring request to remove g++-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove g++-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-14 which isn't installed dpkg: warning: ignoring request to remove gcc-14-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove isympy-common which isn't installed dpkg: warning: ignoring request to remove isympy3 which isn't installed Purging configuration files for javascript-common (11+nmu1) ... dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev 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 (2.82.4-1) ... dpkg: warning: ignoring request to remove libglib2.0-data 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 libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed Purging configuration files for libldap-common (2.5.18+dfsg-3) ... dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblsan0 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 libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.8-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed Purging configuration files for libsasl2-modules:amd64 (2.1.28+dfsg1-8) ... dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsframe1 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstdc++-14-dev which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove manpages which isn't installed dpkg: warning: ignoring request to remove manpages-dev which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-5) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove publicsuffix which isn't installed dpkg: warning: ignoring request to remove python-biopython-doc which isn't installed Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.12.7-1) ... Purging configuration files for python3-argcomplete (3.5.2-1) ... dpkg: warning: ignoring request to remove python3-argh which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-bs4 which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cssselect which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-gffutils which isn't installed dpkg: warning: ignoring request to remove python3-hisat2 which isn't installed dpkg: warning: ignoring request to remove python3-html5lib which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-importlib-metadata which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-olefile which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-pooch which isn't installed dpkg: warning: ignoring request to remove python3-pybedtools which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-simplejson which isn't installed dpkg: warning: ignoring request to remove python3-soupsieve which isn't installed Purging configuration files for python3-sympy (1.13.3-1) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-webencodings which isn't installed dpkg: warning: ignoring request to remove python3-zipp which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.8-3) ... dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-6) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for shared-mime-info (2.4-5+b1) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23.1) ... Purging configuration files for xdg-user-dirs (0.18-1) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', 'bcftools', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-14', 'cpp-14-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-14', 'g++-14-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-14', 'gcc-14-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'isympy-common', 'isympy3', 'javascript-common', 'krb5-locales', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libglib2.0-data', 'libgomp1:amd64', 'libgpm2:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'libldap-common', 'liblerc4:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'manpages', 'manpages-dev', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl', 'perl-modules-5.40', 'publicsuffix', 'python-biopython-doc', 'python-matplotlib-data', 'python3', 'python3-argcomplete', 'python3-argh', 'python3-attr', 'python3-autocommand', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cssselect', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gffutils', 'python3-hisat2', 'python3-html5lib', 'python3-idna', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-numpy', 'python3-olefile', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-platformdirs', 'python3-pooch', 'python3-pybedtools', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-simplejson', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-webencodings', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'samtools', 'sgml-base', 'shared-mime-info', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xdg-user-dirs', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', 'hisat2'] 3m4.7s DUMP: dpkg: warning: ignoring request to remove hisat2 which isn't installed 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', 'hisat2'] 3m4.7s INFO: Running scripts post_purge 3m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_purge_exceptions'] 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_purge_exceptions'] 3m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', '--pending'] 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--purge', '--pending'] 3m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--remove', '--pending'] 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg', '--remove', '--pending'] 3m4.7s INFO: Running scripts post_test 3m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_test_exceptions'] 3m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'tmp/scripts/post_test_exceptions'] 3m4.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 3m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 3m5.5s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-divert', '--list'] 3m5.5s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 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 3m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'dpkg-divert', '--list'] 3m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'clean'] 3m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpv657eaz2', 'apt-get', 'clean'] 3m5.6s DEBUG: Recording chroot state 3m6.0s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 3m6.0s INFO: PASS: Installation and purging test. 3m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/shm'] 3m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/shm'] 3m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/console'] 3m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/console'] 3m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/ptmx'] 3m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/ptmx'] 3m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/pts'] 3m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/dev/pts'] 3m6.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/proc'] 3m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpv657eaz2/proc'] 3m6.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 3m6.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpv657eaz2'] 3m6.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpv657eaz2 3m6.7s INFO: PASS: All tests. 3m6.7s INFO: piuparts run ends. ret=0 End: 2024-12-23 09:13:52 GMT