Start: 2025-04-09 18:23:30 GMT Package: cutesv Version: 2.1.1-1 Installed-Size: 225 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-scipy, python3-sklearn, python3:any, python3-vcf Description: comprehensive discovery of structural variations of genomic sequences Homepage: https://github.com/tjiangHIT/cuteSV Description-md5: 9edbac2d955018599acd19a7f6e81744 Section: science Priority: optional Filename: pool/main/c/cutesv/cutesv_2.1.1-1_all.deb Size: 37364 MD5sum: c3e5f836522a04d64dbcad4043960d15 SHA256: 2d1784f6e00def897b58760f05e547b53ec3bd1c19a015e166a5d2a2f638458f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt cutesv=2.1.1-1 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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt cutesv=2.1.1-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpke3g2hk6 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpke3g2hk6 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/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/tmpke3g2hk6/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/tmpke3g2hk6/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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/tmpke3g2hk6/tmp/scripts/ 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpke3g2hk6/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'update'] 0m2.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7417 kB] Fetched 17.8 MB in 2s (11.6 MB/s) Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash coreutils libssl3t64 openssl-provider-legacy 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7251 kB of archives. After this operation, 824 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-2 [1500 kB] Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB] Get:3 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB] Fetched 7251 kB in 0s (151 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 ... 4927 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-2_amd64.deb ... Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ... Setting up bash (5.2.37-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 4926 files and directories currently installed.) Preparing to unpack .../coreutils_9.7-1_amd64.deb ... Unpacking coreutils (9.7-1) over (9.6-2) ... Setting up coreutils (9.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.0-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.0-1) over (3.4.1-1) ... Setting up openssl-provider-legacy (3.5.0-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.0-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.0-1) over (3.4.1-1) ... Setting up libssl3t64:amd64 (3.5.0-1) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.41-6) ... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 31e44ff00e610efb534d9d62a0a21228 - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_fake-essential'] 0m4.4s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Reading state information... init-system-helpers is already the newest version (1.68). The following additional packages will be installed: libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks Recommended packages: libgpm2 psmisc linux-sysctl-defaults The following NEW packages will be installed: dbconfig-common libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 1757 kB of archives. After this operation, 4947 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:6 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:7 http://deb.debian.org/debian sid/main amd64 ucf all 3.0051 [42.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB] Preconfiguring packages ... Fetched 1757 kB in 0s (64.9 MB/s) Selecting previously unselected package libncursesw6: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 ... 4925 files and directories currently installed.) Preparing to unpack .../0-libncursesw6_6.5+20250216-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libtext-charwidth-perl:amd64. Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b4_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../5-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../6-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../7-dbconfig-common_2.0.24_all.deb ... Unpacking dbconfig-common (2.0.24) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up sensible-utils (0.0.24) ... Setting up procps (2:4.0.4-7) ... Setting up ucf (3.0051) ... Setting up dbconfig-common (2.0.24) ... Creating config file /etc/dbconfig-common/config with new version Processing triggers for libc-bin (2.41-6) ... 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_fake-essential'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s 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' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_minimize'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_setup_zz_backports'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 0m4.4s DEBUG: Recording chroot state 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.7s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed coreutils coreutils 9.7-1 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-3 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-3 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed procps procps 2:4.0.4-7 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-1 install ok installed ucf ucf 3.0051 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-divert', '--list'] 0m4.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-divert', '--list'] 0m4.7s INFO: Running scripts is_testable 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/is_testable_uninstallable'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/is_testable_uninstallable'] 0m4.7s INFO: apt-cache does not know about any of the requested packages 0m4.7s INFO: Running scripts pre_test 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_test_root_password'] 0m4.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_test_root_password'] 0m4.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m5.1s DEBUG: No broken symlinks as far as we can find. 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'show', '--no-all-versions', 'cutesv=2.1.1-1'] 0m5.7s DUMP: Package: cutesv Version: 2.1.1-1 Installed-Size: 225 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-scipy, python3-sklearn, python3:any, python3-vcf Description-en: comprehensive discovery of structural variations of genomic sequences Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. . cuteSV is a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. Description-md5: 9edbac2d955018599acd19a7f6e81744 Homepage: https://github.com/tjiangHIT/cuteSV Section: science Priority: optional Filename: pool/main/c/cutesv/cutesv_2.1.1-1_all.deb Size: 37364 MD5sum: c3e5f836522a04d64dbcad4043960d15 SHA256: 2d1784f6e00def897b58760f05e547b53ec3bd1c19a015e166a5d2a2f638458f 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'show', '--no-all-versions', 'cutesv=2.1.1-1'] 0m5.7s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-scipy, python3-sklearn, python3:any, python3-vcf Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m5.7s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp7xyny_om/piuparts-depends-dummy'] 0m5.7s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp7xyny_om/piuparts-depends-dummy.deb'. 0m5.7s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp7xyny_om/piuparts-depends-dummy'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.7s DUMP: 3.0.0 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.7s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp7xyny_om/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpke3g2hk6/tmp 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m33.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase python3 python3-biopython python3-cairo python3-chardet python3-cigar python3-decorator python3-freetype python3-joblib python3-minimal python3-numpy python3-numpy-dev python3-pil python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-vcf python3.13 python3.13-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre low-memory-monitor gnutls-bin krb5-doc krb5-user liblcms2-utils python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-igraph raxml samtools t-coffee wise python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc ipython3 python3.13-venv python3.13-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: ca-certificates libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common publicsuffix libsasl2-modules python-biopython-doc ncbi-blast+ python3-psutil python3-pytest python3-olefile fonts-dejavu-extra g++ | c++-compiler python3-pooch python3-yaml python3-matplotlib The following NEW packages will be installed: fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase piuparts-depends-dummy python3 python3-biopython python3-cairo python3-chardet python3-cigar python3-decorator python3-freetype python3-joblib python3-minimal python3-numpy python3-numpy-dev python3-pil python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-vcf python3.13 python3.13-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 71.8 MB/71.8 MB of archives. After this operation, 297 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [674 B] Get:2 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.3-1 [861 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.3-1 [2210 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 media-types all 13.0.0 [29.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.3-1 [1954 kB] Get:12 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.3-1 [751 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:18 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:19 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:20 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:21 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:22 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:27 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+24 [217 kB] Get:28 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:29 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:30 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:31 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:33 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-5 [9316 B] Get:54 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:64 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:78 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:79 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:87 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:88 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get:89 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.27.0-2 [114 kB] Get:90 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:92 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.3.1-1 [1158 kB] Get:93 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:94 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:95 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.85+dfsg-2+b1 [1672 kB] Get:96 http://deb.debian.org/debian sid/main amd64 python3-cigar all 0.1.3-2 [5468 B] Get:97 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.2.1-1 [32.9 kB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-joblib all 1.4.2-3 [216 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB] Get:101 http://deb.debian.org/debian sid/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [3980 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-sklearn all 1.4.2+dfsg-8 [2248 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-11+b1 [53.6 kB] Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../6-libpython3.13-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../7-python3.13_3.13.3-1_amd64.deb ... Unpacking python3.13 (3.13.3-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking liblcms2-2:amd64 (2.16-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../65-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../66-libopenjp2-7_2.5.3-2_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.3-2) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../67-libraqm0_0.10.2-1_amd64.deb ... Unpacking libraqm0:amd64 (0.10.2-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../68-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../69-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../70-libtiff6_4.7.0-3_amd64.deb ... Unpacking libtiff6:amd64 (4.7.0-3) ... 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Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../77-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../78-python3-reportlab_4.3.1-1_all.deb ... Unpacking python3-reportlab (4.3.1-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../79-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../80-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../81-python3-biopython_1.85+dfsg-2+b1_amd64.deb ... Unpacking python3-biopython (1.85+dfsg-2+b1) ... Selecting previously unselected package python3-cigar. Preparing to unpack .../82-python3-cigar_0.1.3-2_all.deb ... Unpacking python3-cigar (0.1.3-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../83-python3-decorator_5.2.1-1_all.deb ... Unpacking python3-decorator (5.2.1-1) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../84-python3-joblib_1.4.2-3_all.deb ... Unpacking python3-joblib (1.4.2-3) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../85-python3-pysam_0.23.0+ds-1+b1_amd64.deb ... Unpacking python3-pysam (0.23.0+ds-1+b1) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../86-python3-scipy_1.15.2-7_amd64.deb ... Unpacking python3-scipy (1.15.2-7) ... Selecting previously unselected package python3-threadpoolctl. Preparing to unpack .../87-python3-threadpoolctl_3.1.0-1_all.deb ... Unpacking python3-threadpoolctl (3.1.0-1) ... Selecting previously unselected package python3-sklearn-lib:amd64. Preparing to unpack .../88-python3-sklearn-lib_1.4.2+dfsg-8_amd64.deb ... Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... Selecting previously unselected package python3-sklearn. Preparing to unpack .../89-python3-sklearn_1.4.2+dfsg-8_all.deb ... Unpacking python3-sklearn (1.4.2+dfsg-8) ... Selecting previously unselected package python3-vcf. Preparing to unpack .../90-python3-vcf_0.6.8+git20170215.476169c-11+b1_amd64.deb ... Unpacking python3-vcf (0.6.8+git20170215.476169c-11+b1) ... Selecting previously unselected package piuparts-depends-dummy. Preparing to unpack .../91-piuparts-depends-dummy.deb ... Unpacking piuparts-depends-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up media-types (13.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-5) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-1+b1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libfontenc1:amd64 (1:1.1.8-1+b2) ... Setting up libblas3:amd64 (3.12.1-2) ... 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 (1:2.1.5-3.1) ... Setting up libx11-data (2:1.8.12-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.47-1.1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up libtiff6:amd64 (4.7.0-3) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libopenjp2-7:amd64 (2.5.3-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up readline-common (8.2-6) ... Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... 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 (1:0.9.12-1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libglib2.0-0t64:amd64 (2.84.1-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-1) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.3-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.3-1) ... Setting up python3-cigar (0.1.3-2) ... Setting up python3-freetype (2.5.1-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3-decorator (5.2.1-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up python3-scipy (1.15.2-7) ... Setting up python3-cairo (1.27.0-2) ... Setting up python3-joblib (1.4.2-3) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-1) ... Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-sklearn (1.4.2+dfsg-8) ... Setting up python3-reportlab (4.3.1-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up python3-vcf (0.6.8+git20170215.476169c-11+b1) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-2+b1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m33.9s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m33.9s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpke3g2hk6/./tmp/piuparts-depends-dummy.deb 0m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m33.9s DUMP: piuparts-depends-dummy install ok installed 0m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m34.0s DUMP: (Reading database ... 13352 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 0m34.0s DEBUG: Recording chroot state 0m34.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m34.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m35.6s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m36.0s 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: 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m36.1s DUMP: cutesv: Installed: (none) Candidate: 2.1.1-1 Version table: 2.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', 'cutesv=2.1.1-1'] 0m36.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: cutesv 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 37.4 kB of archives. After this operation, 230 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 cutesv all 2.1.1-1 [37.4 kB] Fetched 37.4 kB in 0s (246 kB/s) Selecting previously unselected package cutesv. (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 ... 13352 files and directories currently installed.) Preparing to unpack .../cutesv_2.1.1-1_all.deb ... Unpacking cutesv (2.1.1-1) ... Setting up cutesv (2.1.1-1) ... 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', 'cutesv=2.1.1-1'] 0m36.7s INFO: Running scripts post_install 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m36.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'systemd-tmpfiles', '--cat-config'] 0m36.8s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 0m36.8s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'systemd-tmpfiles', '--cat-config'] 0m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'remove', 'cutesv'] 0m37.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libtasn1-6 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase python3 python3-biopython python3-cairo python3-chardet python3-cigar python3-decorator python3-freetype python3-joblib python3-minimal python3-numpy python3-numpy-dev python3-pil python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-vcf python3.13 python3.13-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: cutesv 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 230 kB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13374 files and directories currently installed.) Removing cutesv (2.1.1-1) ... 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'remove', 'cutesv'] 0m37.2s INFO: Reinstalling after remove 0m37.2s INFO: Running scripts pre_install 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m37.3s 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: 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m37.3s DUMP: cutesv: Installed: (none) Candidate: 2.1.1-1 Version table: 2.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m37.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m37.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', 'cutesv=2.1.1-1'] 0m37.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: cutesv 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/37.4 kB of archives. After this operation, 230 kB of additional disk space will be used. Selecting previously unselected package cutesv. (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 ... 13352 files and directories currently installed.) Preparing to unpack .../cutesv_2.1.1-1_all.deb ... Unpacking cutesv (2.1.1-1) ... Setting up cutesv (2.1.1-1) ... 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', 'cutesv=2.1.1-1'] 0m37.8s INFO: Running scripts post_install 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m37.8s INFO: Running scripts pre_install 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_database-server'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_exceptions'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_extras'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m37.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m37.9s DUMP: cutesv: Installed: 2.1.1-1 Candidate: 2.1.1-1 Version table: *** 2.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-cache', 'policy', 'cutesv'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', '--reinstall', 'cutesv=2.1.1-1'] 0m38.4s DUMP: Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/37.4 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 13374 files and directories currently installed.) Preparing to unpack .../cutesv_2.1.1-1_all.deb ... Unpacking cutesv (2.1.1-1) over (2.1.1-1) ... Setting up cutesv (2.1.1-1) ... 0m38.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', '-y', 'install', '--reinstall', 'cutesv=2.1.1-1'] 0m38.4s INFO: Running scripts post_install 0m38.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m38.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_install_exceptions'] 0m38.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m39.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 0m39.7s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf (python3-reportlab) 0m40.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', '-ac', '--ignore-obsolete'] 0m41.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', '-ac', '--ignore-obsolete'] 0m41.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m41.2s DUMP: 0.15.6 0m41.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m41.2s INFO: Running adequate version 0.15.6 now. 0m41.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'cutesv'] 0m41.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'cutesv'] 0m41.2s INFO: Running scripts pre_remove 0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_exceptions'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_exceptions'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.3s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed coreutils coreutils 9.7-1 install ok installed cutesv cutesv 2.1.1-1 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig-config fontconfig-config 2.15.0-2.3 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-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.41-3 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.13.0-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libexpat1:amd64 libexpat1 2.7.1-1 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 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 1:2.1.5-3.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-5 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.3-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.3-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.3-1 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtiff6:amd64 libtiff6 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed mount mount 2.41-3 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed procps procps 2:4.0.4-7 install ok installed python3 python3 3.13.3-1 install ok installed python3-biopython python3-biopython 1.85+dfsg-2+b1 install ok installed python3-cairo python3-cairo 1.27.0-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-cigar python3-cigar 0.1.3-2 install ok installed python3-decorator python3-decorator 5.2.1-1 install ok installed python3-freetype python3-freetype 2.5.1-1 install ok installed python3-joblib python3-joblib 1.4.2-3 install ok installed python3-minimal python3-minimal 3.13.3-1 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-pil:amd64 python3-pil 11.1.0-5+b1 install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1 install ok installed python3-reportlab python3-reportlab 4.3.1-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.15.2-7 install ok installed python3-sklearn python3-sklearn 1.4.2+dfsg-8 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.4.2+dfsg-8 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-vcf python3-vcf 0.6.8+git20170215.476169c-11+b1 install ok installed python3.13 python3.13 3.13.3-1 install ok installed python3.13-minimal python3.13-minimal 3.13.3-1 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sgml-base sgml-base 1.31 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-1 install ok installed ucf ucf 3.0051 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'remove', '--allow-remove-essential', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtiff6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-cigar', 'python3-decorator', 'python3-freetype', 'python3-joblib', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'cutesv'] 1m0.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: cutesv fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 libatomic1 libblas3 libbrotli1 libcairo2 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3t64 libhtscodecs2 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libopenjp2-7 libp11-kit0 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh2-1t64 libtasn1-6 libtiff6 libunistring5 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 media-types netbase python3 python3-biopython python3-cairo python3-chardet python3-cigar python3-decorator python3-freetype python3-joblib python3-minimal python3-numpy python3-numpy-dev python3-pil python3-pysam python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-vcf python3.13 python3.13-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 104 to remove and 0 not upgraded. After this operation, 297 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 ... 13374 files and directories currently installed.) Removing cutesv (2.1.1-1) ... Removing python3-biopython (1.85+dfsg-2+b1) ... Removing python3-reportlab (4.3.1-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.27.0-2) ... Removing libcairo2:amd64 (1.18.4-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-2.3) ... Removing fontconfig-config (2.15.0-2.3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-8) ... Removing python3-pil:amd64 (11.1.0-5+b1) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libglib2.0-0t64:amd64 (2.84.1-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing python3-sklearn (1.4.2+dfsg-8) ... Removing python3-scipy (1.15.2-7) ... Removing python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libblas3:amd64 (3.12.1-2) ... Removing xfonts-utils (1:7.7+7) ... Removing python3-freetype (2.5.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing python3-vcf (0.6.8+git20170215.476169c-11+b1) ... Removing python3-pysam (0.23.0+ds-1+b1) ... Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.13.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-1+b1) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing python3-decorator (5.2.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libfontenc1:amd64 (1:1.1.8-1+b2) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-5) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.9+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing libopenjp2-7:amd64 (2.5.3-2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.47-1.1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libwebpmux3:amd64 (1.5.0-0.1) ... Removing libwebpdemux2:amd64 (1.5.0-0.1) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-cigar (0.1.3-2) ... Removing python3-joblib (1.4.2-3) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing python3 (3.13.3-1) ... Removing python3-minimal (3.13.3-1) ... Removing python3.13 (3.13.3-1) ... Removing python3.13-minimal (3.13.3-1) ... Removing libexpat1:amd64 (2.7.1-1) ... Removing libpython3-stdlib:amd64 (3.13.3-1) ... Removing libpython3.13-stdlib:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libgnutls30t64:amd64 (3.8.9-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libffi8:amd64 (3.4.7-1) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libpython3.13-minimal:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-2) ... Removing media-types (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.2-6) ... Processing triggers for libc-bin (2.41-6) ... 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'remove', '--allow-remove-essential', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtiff6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-cigar', 'python3-decorator', 'python3-freetype', 'python3-joblib', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'cutesv'] 1m0.9s INFO: Running scripts post_remove 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_remove_cleanup'] 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_remove_cleanup'] 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_remove_exceptions'] 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_remove_exceptions'] 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtiff6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-cigar', 'python3-decorator', 'python3-freetype', 'python3-joblib', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m1.1s DUMP: (Reading database ... 5529 files and directories currently installed.) Purging configuration files for fontconfig-config (2.15.0-2.3) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... Purging configuration files for fonts-urw-base35 (20200910-8) ... 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 libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcom-err2 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 libffi8 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.84.1-1) ... dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ... 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 libidn2-0 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 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 liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 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 libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.3-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed 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 libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for media-types (13.0.0) ... Purging configuration files for netbase (6.5) ... Purging configuration files for python3 (3.13.3-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-cigar which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed Purging configuration files for python3-numpy (1:2.2.4+ds-1) ... dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-sklearn which isn't installed dpkg: warning: ignoring request to remove python3-sklearn-lib which isn't installed dpkg: warning: ignoring request to remove python3-threadpoolctl which isn't installed dpkg: warning: ignoring request to remove python3-vcf which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.3-1) ... Purging configuration files for readline-common (8.2-6) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+24) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+7) ... Purging configuration files for xml-core (0.19) ... 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libtiff6:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxrender1:amd64', 'media-types', 'netbase', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-cigar', 'python3-decorator', 'python3-freetype', 'python3-joblib', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pil:amd64', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.13', 'python3.13-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'cutesv'] 1m1.1s DUMP: dpkg: warning: ignoring request to remove cutesv which isn't installed 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', 'cutesv'] 1m1.1s INFO: Running scripts post_purge 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_purge_exceptions'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_purge_exceptions'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_purge_manual_cleanup'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_purge_manual_cleanup'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', '--pending'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--purge', '--pending'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--remove', '--pending'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg', '--remove', '--pending'] 1m1.1s INFO: Running scripts post_test 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_test_exceptions'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'tmp/scripts/post_test_exceptions'] 1m1.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 1m1.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 1m1.6s DEBUG: No broken symlinks as far as we can find. 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-divert', '--list'] 1m1.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'dpkg-divert', '--list'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6', 'apt-get', 'clean'] 1m1.6s DEBUG: Recording chroot state 1m2.3s INFO: PASS: Installation and purging test. 1m2.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/shm'] 1m2.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/shm'] 1m2.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/console'] 1m2.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/console'] 1m2.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/ptmx'] 1m2.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/ptmx'] 1m2.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/pts'] 1m2.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/dev/pts'] 1m2.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/proc'] 1m2.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6/proc'] 1m2.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 1m2.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpke3g2hk6'] 1m2.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpke3g2hk6 1m2.6s INFO: PASS: All tests. 1m2.6s INFO: piuparts run ends. ret=0 End: 2025-04-09 18:24:33 GMT