Start: 2024-11-19 03:48:34 GMT [testing] Package: python3-pairtools Source: pairtools (1.0.3-1) Version: 1.0.3-1+b2 Installed-Size: 796 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.13), python3 (>= 3.12~), python3-bioframe, python3-click, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any Suggests: python3-pairtools-examples (>= 1.0.2) Description: Framework to process sequencing data from a Hi-C experiment Homepage: https://github.com/mirnylab/pairtools Description-md5: a340132b5467a45fa9b90e04ece3e5c1 Section: python Priority: optional Filename: pool/main/p/pairtools/python3-pairtools_1.0.3-1+b2_amd64.deb Size: 200080 MD5sum: 63c0b514c1257c161972b39c7ce015fd SHA256: 10b888e7c0035d058bad8282d04b6e723aa1f57a5185f01678fddf92db5d4115 [sid] Package: python3-pairtools Source: pairtools Version: 1.1.0-1 Installed-Size: 1266 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.12~), python3-bioframe, python3-click, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any Suggests: python3-pairtools-examples (>= 1.0.2) Description: Framework to process sequencing data from a Hi-C experiment Homepage: https://github.com/mirnylab/pairtools Description-md5: a340132b5467a45fa9b90e04ece3e5c1 Section: python Priority: optional Filename: pool/main/p/pairtools/python3-pairtools_1.1.0-1_amd64.deb Size: 262192 MD5sum: 03b65da8ee9c9f413ece20087cca8042 SHA256: dfe66150e5452117f500b48a6ccd0004d1233cce6da4b3571ce1f1e190a777b9 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-pairtools=1.1.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-pairtools=1.1.0-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmpi7_o5fn_ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpi7_o5fn_ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpi7_o5fn_/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9376 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6265 kB] Fetched 15.8 MB in 1s (18.2 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bsdutils debianutils libblkid1 libgnutls30t64 libmount1 libsmartcols1 libuuid1 login mount util-linux 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3643 kB of archives. After this operation, 9216 B disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.21 [92.1 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-11 [168 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-11 [199 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-11 [1213 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-11 [155 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.2-11 [81.5 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3643 kB in 0s (77.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5158 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-11_amd64.deb ... Unpacking bsdutils (1:2.40.2-11) over (1:2.40.2-9) ... Setting up bsdutils (1:2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../debianutils_5.21_amd64.deb ... Unpacking debianutils (5.21) over (5.20) ... Setting up debianutils (5.21) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-11_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libuuid1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-11_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libblkid1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-11_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libmount1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-11_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libsmartcols1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-11_amd64.deb ... Unpacking util-linux (2.40.2-11) over (2.40.2-9) ... Setting up util-linux (2.40.2-11) ... (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 ... 5155 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-11_amd64.deb ... Unpacking mount (2.40.2-11) over (2.40.2-9) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-11_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-11) over (1:4.16.0-2+really2.40.2-9) ... Preparing to unpack .../libgnutls30t64_3.8.8-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.8-2) over (3.8.6-2+b1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up mount (2.40.2-11) ... Setting up login (1:4.16.0-2+really2.40.2-11) ... Processing triggers for libc-bin (2.40-3) ... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 7a415e9579e6f7162aebaa573423b254 - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s 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 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s 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' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 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 1.47.1-1+b1 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 1.12-1.1 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 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 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 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 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-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 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 2.40.2-11 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 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 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 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 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 256.7-3 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 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 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+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 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 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-7 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-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools'] 0m3.5s DUMP: Package: python3-pairtools Source: pairtools (1.0.3-1) Version: 1.0.3-1+b2 Installed-Size: 796 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.13), python3 (>= 3.12~), python3-bioframe, python3-click, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any Suggests: python3-pairtools-examples (>= 1.0.2) Description-en: Framework to process sequencing data from a Hi-C experiment Simple and fast command-line framework to process sequencing data from a Hi-C experiment. . Process pair-end sequence alignments and perform the following operations: . - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules - Sort .pairs files for downstream analyses - Detect, tag and remove PCR/optical duplicates - Generate extensive statistics of Hi-C datasets - Select Hi-C pairs given flexibly defined criteria - Restore .sam alignments from Hi-C pairs Description-md5: a340132b5467a45fa9b90e04ece3e5c1 Homepage: https://github.com/mirnylab/pairtools Section: python Priority: optional Filename: pool/main/p/pairtools/python3-pairtools_1.0.3-1+b2_amd64.deb Size: 200080 MD5sum: 63c0b514c1257c161972b39c7ce015fd SHA256: 10b888e7c0035d058bad8282d04b6e723aa1f57a5185f01678fddf92db5d4115 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools'] 0m3.5s INFO: apt-cache knows about the following packages: python3-pairtools 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m3.5s 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: 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m3.5s DUMP: python3-pairtools: Installed: (none) Candidate: 1.0.3-1+b2 Version table: 1.0.3-1+b2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools'] 0m31.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libatomic1 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 media-types netbase openssl python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-bioframe python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-fs python3-idna 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-packaging python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-pysam python3-requests python3-scipy python3-six python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-yaml python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common tk8.6-blt2.5 unicode-data x11-common Suggested packages: blt-demo low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-venv python-attr-doc python-charset-normalizer-doc python-cycler-doc 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 gcc gfortran python-numpy-doc python3-dev python3-pytest python3-pairtools-examples python-pandas-doc python3-statsmodels python-pil-doc python3-setuptools python-pyparsing-doc 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 binutils binfmt-support readline-doc Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules python3-bs4 python3-cssselect python3-html5lib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-jinja2 python3-numba python3-olefile g++ | c++-compiler isympy-common The following NEW packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libatomic1 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 media-types netbase openssl python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-bioframe python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-fs python3-idna 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-packaging python3-pairtools python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-pysam python3-requests python3-scipy python3-six python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-yaml python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common tk8.6-blt2.5 unicode-data x11-common 0 upgraded, 141 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After this operation, 522 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 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 3.12.7-3 [2162 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 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 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [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 3.12.7-3 [1966 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:46 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:48 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-2 [103 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2+b1 [264 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:111 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b5 [25.6 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4+b1 [1631 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:131 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 python3-bioframe all 0.4.1-1 [71.6 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.1.7-2 [94.3 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 python3-pairtools amd64 1.0.3-1+b2 [200 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 106 MB in 4s (25.5 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 ... 5158 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... 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_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 5478 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... 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 (8.2-5) ... 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_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 6036 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../003-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../004-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../005-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../006-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../009-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../010-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../011-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../012-libxdmcp6_1%3a1.1.2-3+b2_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b2) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../013-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. 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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 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 libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... 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 libblas3:amd64 (3.12.0-3+b1) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... 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 (1.4.0-1+b1) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... 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 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 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 (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... 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+b2) ... 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 ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... 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 (3.12.7-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up python3.13-tk (3.13.0-2) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.7-3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... 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-urllib3 (2.0.7-2) ... 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-appdirs (1.4.4-4) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b5) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-tk:amd64 (3.12.7-1) ... Setting up python3-click (8.1.7-2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-fs (2.4.16-4) ... 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-contourpy (1.3.0-2+b1) ... Setting up python3-scipy (1.13.1-6) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.54.1-4+b1) ... Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-bioframe (0.4.1-1) ... Setting up python3-pairtools (1.0.3-1+b2) ... /usr/lib/python3/dist-packages/pairtools/cli/select.py:90: SyntaxWarning: invalid escape sequence '\d' """Select pairs according to some condition. /usr/lib/python3/dist-packages/pairtools/lib/stats.py:928: SyntaxWarning: invalid escape sequence '\w' """Extract the name of the tile for each read name in the series Processing triggers for libc-bin (2.40-3) ... 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. 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools'] 0m31.7s INFO: Running scripts post_install 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m31.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m32.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m32.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpi7_o5fn_ to sid 0m32.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m32.5s INFO: Running scripts pre_distupgrade 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_exceptions'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'update'] 0m34.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7335 kB] Fetched 17.6 MB in 2s (10.1 MB/s) Reading package lists... 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'update'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-yf', 'dist-upgrade'] 0m37.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 libaudit-common libaudit1 libglib2.0-0t64 libpcre2-8-0 libpython3-stdlib libsystemd0 libudev1 login.defs passwd python3 python3-attr python3-fonttools python3-minimal python3-packaging python3-pairtools python3-pkg-resources 18 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8558 kB of archives. After this operation, 444 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc2-3 [447 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc2-3 [147 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.12 [1042 kB] Get:4 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.12 [1364 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:6 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:8 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] Get:11 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-5 [185 kB] Get:12 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-5 [1232 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.55.0-1 [1634 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3-pairtools amd64 1.1.0-1 [262 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8558 kB in 0s (68.3 MB/s) (Reading database ... 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(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 ... 17163 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.2-2_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.2-2) over (1:4.0.1-3) ... Setting up libaudit1:amd64 (1:4.0.2-2) ... (Reading database ... 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Preparing to unpack .../3-python3-attr_24.2.0-1_all.deb ... Unpacking python3-attr (24.2.0-1) over (23.2.0-2) ... Preparing to unpack .../4-python3-pkg-resources_75.2.0-1_all.deb ... Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-2) ... Preparing to unpack .../5-python3-fonttools_4.55.0-1_amd64.deb ... Unpacking python3-fonttools (4.55.0-1) over (4.54.1-4+b1) ... Preparing to unpack .../6-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) over (24.1-1) ... Preparing to unpack .../7-python3-pairtools_1.1.0-1_amd64.deb ... Unpacking python3-pairtools (1.1.0-1) over (1.0.3-1+b2) ... Setting up login.defs (1:4.16.0-5) ... Installing new version of config file /etc/login.defs ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up passwd (1:4.16.0-5) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-pairtools (1.1.0-1) ... Setting up python3-fonttools (4.55.0-1) ... Processing triggers for libc-bin (2.40-3) ... 0m37.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-yf', 'dist-upgrade'] 0m37.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m38.2s DUMP: e73727d22e96307957a612d044fbedbf - 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools'] 0m38.3s DUMP: Package: python3-pairtools Source: pairtools Version: 1.1.0-1 Installed-Size: 1266 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.14), python3 (>= 3.12~), python3-bioframe, python3-click, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-scipy, python3-yaml, python3:any Suggests: python3-pairtools-examples (>= 1.0.2) Description-en: Framework to process sequencing data from a Hi-C experiment Simple and fast command-line framework to process sequencing data from a Hi-C experiment. . Process pair-end sequence alignments and perform the following operations: . - Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules - Sort .pairs files for downstream analyses - Detect, tag and remove PCR/optical duplicates - Generate extensive statistics of Hi-C datasets - Select Hi-C pairs given flexibly defined criteria - Restore .sam alignments from Hi-C pairs Description-md5: a340132b5467a45fa9b90e04ece3e5c1 Homepage: https://github.com/mirnylab/pairtools Section: python Priority: optional Filename: pool/main/p/pairtools/python3-pairtools_1.1.0-1_amd64.deb Size: 262192 MD5sum: 03b65da8ee9c9f413ece20087cca8042 SHA256: dfe66150e5452117f500b48a6ccd0004d1233cce6da4b3571ce1f1e190a777b9 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'show', '--no-all-versions', 'python3-pairtools'] 0m38.3s INFO: apt-cache knows about the following packages: python3-pairtools 0m38.3s INFO: Running scripts pre_install 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m38.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m38.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m38.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m38.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m38.4s DUMP: python3-pairtools: Installed: 1.1.0-1 Candidate: 1.1.0-1 Version table: *** 1.1.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m38.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m38.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools'] 0m38.6s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pairtools is already the newest version (1.1.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools'] 0m38.6s INFO: Running scripts post_install 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m38.6s INFO: Running scripts post_distupgrade 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_exceptions'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_exceptions'] 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_distupgrade_zz_backports'] 0m38.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m39.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m39.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m40.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m40.1s INFO: Running scripts pre_install 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_database-server'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_exceptions'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_extras'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m40.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m40.2s DUMP: python3-pairtools: Installed: 1.1.0-1 Candidate: 1.1.0-1 Version table: *** 1.1.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-cache', 'policy', 'python3-pairtools'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools=1.1.0-1'] 0m40.5s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pairtools is already the newest version (1.1.0-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', '-y', 'install', 'python3-pairtools=1.1.0-1'] 0m40.5s INFO: Running scripts post_install 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_install_exceptions'] 0m40.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m41.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m41.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', '-ac', '--ignore-obsolete'] 0m43.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', '-ac', '--ignore-obsolete'] 0m43.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.4s DUMP: 0.15.6 0m43.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m43.4s INFO: Running adequate version 0.15.6 now. 0m43.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'python3-pairtools'] 0m43.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'python3-pairtools'] 0m43.5s INFO: Running scripts pre_remove 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_exceptions'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/pre_remove_exceptions'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m44.9s DUMP: install ok installed apt apt 2.9.12 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 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 1.47.1-1+b1 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-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 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 1.12-1.1 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 2.9.12 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 libblas3:amd64 libblas3 3.12.0-3+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.0-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 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 1.47.1-1+b1 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 libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 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 libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 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 1.50-4 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 10.0.1-1 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 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 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 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 3.12.0-3+b1 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 liblerc4:amd64 liblerc4 4.0.0+ds-5 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 2.40.2-11 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 1.4.0-1+b1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 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 10.44-4 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 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 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 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-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 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 libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 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++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 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 libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 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 libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 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+b2 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 libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 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 2.40.2-11 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 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-7 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-appdirs python3-appdirs 1.4.4-4 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-bioframe python3-bioframe 0.4.1-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 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-click python3-click 8.1.7-2 install ok installed python3-colorama python3-colorama 0.4.6-4 install ok installed python3-contourpy python3-contourpy 1.3.0-2+b1 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 4.55.0-1 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-idna python3-idna 3.8-2 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 4.0.2+dfsg-1+b5 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-packaging python3-packaging 24.2-1 install ok installed python3-pairtools python3-pairtools 1.1.0-1 install ok installed python3-pandas python3-pandas 2.2.3+dfsg-5 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-5+b1 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 75.2.0-1 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-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-scipy python3-scipy 1.13.1-6 install ok installed python3-six python3-six 1.16.0-7 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-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 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3-yaml python3-yaml 6.0.2-1+b1 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed python3.12-tk python3.12-tk 3.12.7-3 install ok installed python3.13-tk python3.13-tk 3.13.0-2 install ok installed readline-common readline-common 8.2-5 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 tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024b-3 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 2.40.2-11 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-bioframe', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-fs', 'python3-idna', '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-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-yaml', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'python3-pairtools'] 0m48.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libatomic1 libblas3 libbrotli1 libcurl3t64-gnutls libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libopenjp2-7 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libqhull-r8.0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1t64 libtcl8.6 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 media-types netbase openssl python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-bioframe python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-contourpy python3-cycler python3-dateutil python3-decorator python3-fonttools python3-fs python3-idna 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-packaging python3-pairtools python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-pysam python3-requests python3-scipy python3-six python3-sympy python3-tk python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-yaml python3.12 python3.12-minimal python3.12-tk python3.13-tk readline-common tk8.6-blt2.5 unicode-data x11-common 0 upgraded, 0 newly installed, 141 to remove and 0 not upgraded. After this operation, 523 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 ... 17168 files and directories currently installed.) Removing python3-pairtools (1.1.0-1) ... Removing python3-bioframe (0.4.1-1) ... 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-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 tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.0-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing fonts-lyx (2.4.2.1-1) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing python3-pandas (2.2.3+dfsg-5) ... Removing python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Removing python3-contourpy (1.3.0-2+b1) ... Removing python3-pysam (0.22.1+ds-2+b2) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.11.0-1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing python3-yaml (6.0.2-1+b1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.4.0-1+b1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... 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 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 libssh2-1t64:amd64 (1.11.1-1) ... Removing python3.12-tk (3.12.7-3) ... Removing libyaml-0-2:amd64 (0.2.5-1+b2) ... Removing openssl (3.3.2-2) ... Removing python3-charset-normalizer (3.4.0-1+b1) ... Removing python3-click (8.1.7-2) ... Removing python3-colorama (0.4.6-4) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-idna (3.8-2) ... Removing python3-kiwisolver (1.4.7-2+b1) ... Removing python3-packaging (24.2-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-urllib3 (2.0.7-2) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... 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 (1:1.1.2-3+b2) ... Removing python3-ufolib2 (0.16.1+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3-fonttools (4.55.0-1) ... Removing python3-scipy (1.13.1-6) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-3+b1) ... Removing libblas3:amd64 (3.12.0-3+b1) ... Removing python3-sympy (1.13.3-1) ... Removing python3-fs (2.4.16-4) ... Removing python3-pkg-resources (75.2.0-1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-six (1.16.0-7) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... 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-appdirs (1.4.4-4) ... 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 (4.0.2+dfsg-1+b5) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... 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 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... 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 (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-bioframe', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-fs', 'python3-idna', '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-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-yaml', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'python3-pairtools'] 0m48.7s INFO: Running scripts post_remove 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_remove_exceptions'] 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_remove_exceptions'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-bioframe', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-fs', 'python3-idna', '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-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-yaml', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common'] 0m48.9s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5202 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. 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) ... 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 dpkg: warning: ignoring request to remove libatomic1 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 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 libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-3) ... dpkg: warning: ignoring request to remove libgomp1 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 libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 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 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 dpkg: warning: ignoring request to remove liblerc4 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 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 (3.12.7-3) ... 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 libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db 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 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 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 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 libyaml-0-2 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-appdirs 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-bioframe which isn't installed dpkg: warning: ignoring request to remove python3-brotli 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-click which isn't installed dpkg: warning: ignoring request to remove python3-colorama which isn't installed dpkg: warning: ignoring request to remove python3-contourpy 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-fs which isn't installed dpkg: warning: ignoring request to remove python3-idna 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-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib 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-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six 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-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-yaml which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... 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 (8.2-5) ... 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 x11-common (1:7.7+23.1) ... 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-lyx', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libyaml-0-2:amd64', 'media-types', 'netbase', 'openssl', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-bioframe', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-fonttools', 'python3-fs', 'python3-idna', '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-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-yaml', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'tk8.6-blt2.5', 'unicode-data', 'x11-common'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', 'python3-pairtools'] 0m48.9s DUMP: dpkg: warning: ignoring request to remove python3-pairtools which isn't installed 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', 'python3-pairtools'] 0m48.9s INFO: Running scripts post_purge 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_purge_exceptions'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_purge_exceptions'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', '--pending'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--purge', '--pending'] 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--remove', '--pending'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg', '--remove', '--pending'] 0m48.9s INFO: Running scripts post_test 0m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_test_exceptions'] 0m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'tmp/scripts/post_test_exceptions'] 0m48.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m49.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-divert', '--list'] 0m49.1s 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 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'dpkg-divert', '--list'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'clean'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_', 'apt-get', 'clean'] 0m49.2s DEBUG: Recording chroot state 0m49.4s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, 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 0m49.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/shm'] 0m49.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/shm'] 0m49.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/console'] 0m49.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/console'] 0m49.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/ptmx'] 0m49.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/ptmx'] 0m49.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts'] 0m49.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/dev/pts'] 0m49.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/proc'] 0m49.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_/proc'] 0m49.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m49.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi7_o5fn_'] 0m49.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpi7_o5fn_ 0m49.8s INFO: PASS: Upgrading between Debian distributions. 0m49.8s INFO: PASS: All tests. 0m49.8s INFO: piuparts run ends. ret=0 End: 2024-11-19 03:49:24 GMT