Start: 2023-12-11 21:23:56 GMT [testing] Package: cutesv Version: 2.0.2-1 Installed-Size: 191 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-vcf, python3:any 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_2.0.2-1_all.deb Size: 32972 MD5sum: 3251614f79eb52d81adb0fa32fffa550 SHA256: 38a00fc3794f1080b39c82f59e39046a6ac8f08d155e69d3cee0b5802af3a550 [sid] Package: cutesv Version: 2.1.0-2 Installed-Size: 222 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-scipy, python3-sklearn, python3-vcf, python3:any 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_2.1.0-2_all.deb Size: 36872 MD5sum: 151d9c85cee35c8ad2cc29047ee88d8d SHA256: a2763c15d8db22f795aa5739351fe04959c5045e26cd06bdbb6610558a4c0777 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt cutesv=2.1.0-2 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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt cutesv=2.1.0-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpcyt5xo04 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpcyt5xo04 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/proc'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/proc'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/ptmx'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/ptmx'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/shm'] 0m1.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpcyt5xo04/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'update'] 0m5.2s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8787 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 2s (6333 kB/s) Reading package lists... 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'update'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libgnutls30 libsystemd0 libudev1 perl-base tzdata 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7179 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u4 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u3 [2755 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u3 [606 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u1 [1404 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.19-1~deb12u1 [331 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.19-1~deb12u1 [108 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7179 kB in 0s (84.5 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 ... 6098 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u4_amd64.deb ... Unpacking base-files (12.4+deb12u4) over (12.4+deb12u2) ... Setting up base-files (12.4+deb12u4) ... Installing new version of config file /etc/debian_version ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../perl-base_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl-base (5.36.0-7+deb12u1) over (5.36.0-7) ... Setting up perl-base (5.36.0-7+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u3_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u3) over (2.36-9+deb12u2) ... Setting up libc6:amd64 (2.36-9+deb12u3) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u3_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u3) over (2.36-9+deb12u2) ... Setting up libc-bin (2.36-9+deb12u3) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u1_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u1) over (3.7.9-2) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.19-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.19-1~deb12u1) over (252.17-1~deb12u1) ... Setting up libsystemd0:amd64 (252.19-1~deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libudev1_252.19-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.19-1~deb12u1) over (252.17-1~deb12u1) ... Setting up libudev1:amd64 (252.19-1~deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) over (2023c-5) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Dec 11 21:24:04 UTC 2023. Universal Time is now: Mon Dec 11 21:24:04 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.36-9+deb12u3) ... 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-yf', 'dist-upgrade'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.0s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.0s INFO: Running scripts post_setup 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_dummy_users'] 0m10.2s 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 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_dummy_users'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_forbid_home'] 0m10.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_forbid_home'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_minimize'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_minimize'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_zz_backports'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_setup_zz_backports'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.3s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.19-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m10.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 0m10.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 0m10.6s INFO: Running scripts is_testable 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s INFO: Running scripts pre_test 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_test_exceptions'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_test_root_password'] 0m10.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_test_root_password'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'show', '--no-all-versions', 'cutesv'] 0m10.9s DUMP: Package: cutesv Version: 2.0.2-1 Installed-Size: 191 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-vcf, python3:any 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_2.0.2-1_all.deb Size: 32972 MD5sum: 3251614f79eb52d81adb0fa32fffa550 SHA256: 38a00fc3794f1080b39c82f59e39046a6ac8f08d155e69d3cee0b5802af3a550 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'show', '--no-all-versions', 'cutesv'] 0m10.9s INFO: apt-cache knows about the following packages: cutesv 0m10.9s INFO: Running scripts pre_install 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 0m11.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.4,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 0m11.1s DUMP: cutesv: Installed: (none) Candidate: 2.0.2-1 Version table: 2.0.2-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 0m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv'] 1m21.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-cigar python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-vcf python3.11 python3.11-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 gdbm-l10n low-memory-monitor krb5-doc krb5-user liblcms2-utils sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl 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-scipy raxml samtools t-coffee wise gcc gfortran python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.11-venv python3.11-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 libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-olefile The following NEW packages will be installed: cutesv fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcurl3-gnutls libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libncursesw6 libnghttp2-14 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-cigar python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-vcf python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 50.3 MB of archives. After this operation, 186 MB of additional disk space will be used. 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bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:18 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 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amd64 2.1.28+dfsg-10 [20.3 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-9+b1 [43.1 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 cutesv all 2.0.2-1 [33.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.3 MB in 3s (19.4 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6100 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... 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 (1:2.1.5-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... 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Setting up liblapack3:amd64 (3.11.0-2) ... 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 libxcb1:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u4) ... Setting up xfonts-utils (1:7.7+6) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up mime-support (3.66) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-cigar (0.1.3-2) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-vcf (0.6.8+git20170215.476169c-9+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up cutesv (2.0.2-1) ... 1m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv'] 1m21.5s INFO: Running scripts post_install 1m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 1m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 1m21.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 1m22.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 1m22.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpcyt5xo04 to sid 1m22.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m22.1s INFO: Running scripts pre_distupgrade 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_exceptions'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_exceptions'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'update'] 1m27.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9596 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7071 kB] Fetched 16.9 MB in 4s (4651 kB/s) Reading package lists... 1m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'update'] 1m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-yf', 'dist-upgrade'] 2m41.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: python3-renderpm python3-reportlab-accel The following NEW packages will be installed: binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-13 fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono g++ g++-13 gcc gcc-13 gcc-13-base libasan8 libatomic1 libbinutils libboost-dev libboost1.74-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libexpat1-dev libfontconfig1 libgcc-13-dev libgprofng0 libhwasan0 libisl23 libitm1 libjansson4 libjs-jquery libjs-sphinxdoc libjs-underscore liblbfgsb0 liblsan0 libmpc3 libmpfr6 libnsl-dev libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libpixman-1-0 libproc2-0 libpython3-all-dev libpython3-dev libpython3.11 libpython3.11-dev libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libsframe1 libsharpyuv0 libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 libunistring5 libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxext6 libxrender1 libxsimd-dev linux-libc-dev netbase procps python3-all python3-all-dev python3-beniget python3-cairo python3-decorator python3-dev python3-distutils python3-freetype python3-gast python3-joblib python3-lib2to3 python3-ply python3-pythran python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3.11-dev python3.12 python3.12-dev python3.12-minimal rpcsvc-proto zlib1g-dev The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils cutesv dash debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base grep init-system-helpers libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libbrotli1 libbsd0 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libcurl3-gnutls libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libffi8 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libhtscodecs2 libidn2-0 libimagequant0 libk5crypto3 libkrb5-3 libkrb5support0 liblerc4 liblzma5 libmd0 libmount1 libncursesw6 libnettle8 libnghttp2-14 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl3 libstdc++6 libsystemd0 libtasn1-6 libtiff6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libwebp7 libwebpdemux2 libwebpmux3 libxxhash0 libzstd1 login logsave mawk media-types mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-vcf python3.11 python3.11-minimal readline-common sysvinit-utils tzdata usr-is-merged util-linux util-linux-extra zlib1g 136 upgraded, 97 newly installed, 2 to remove and 0 not upgraded. Need to get 213 MB of archives. After this operation, 826 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.14 [88.3 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-2 [96.7 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-13 [2753 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-13 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-8 [41.1 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-8 [57.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-2+b1 [2948 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-8 [695 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:15 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.1 [239 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255-1 [360 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255-1 [122 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3 [87.5 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.7 [946 kB] Get:21 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.1 [1561 kB] Get:22 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:23 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:24 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:25 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-3 [431 kB] Get:26 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3 [616 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20231121-1 [135 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20231121-1 [341 kB] Get:29 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20231121-1 [429 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libperl5.36 amd64 5.36.0-10 [4221 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl amd64 5.36.0-10 [239 kB] Get:32 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.36.0-10 [1602 kB] Get:33 http://deb.debian.org/debian sid/main amd64 perl-modules-5.36 all 5.36.0-10 [2815 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-2 [89.7 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [697 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-2 [159 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-1+b1 [74.5 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-2 [190 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-1 [11.2 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.3-3 [16.9 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-1 [48.2 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-2 [116 kB] Get:46 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-2 [155 kB] Get:47 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-2 [1229 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-2 [419 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.4-1+b1 [125 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3 [48.3 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.2-1 [1424 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:57 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1 [65.5 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:60 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b1 [90.3 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1 [49.9 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1 [264 kB] Get:64 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3 [972 kB] Get:65 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:66 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.4-2+b1 [47.1 kB] Get:68 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.7 [1362 kB] Get:69 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 38 [5504 B] Get:70 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:71 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20231121-1 [267 kB] Get:72 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-5 [32.1 kB] Get:73 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.81+dfsg-2+b1 [1624 kB] Get:74 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.0.7-1 [673 kB] Get:75 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:76 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:77 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:78 http://deb.debian.org/debian sid/main amd64 tzdata all 2023c-11 [252 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.4-2 [2058 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:88 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.44.2-1 [882 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-2 [29.6 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:96 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:97 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:99 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b1 [302 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.40-2 [276 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1 [437 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.2.0-8 [131 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3 [71.1 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-1 [1452 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.0.1-1 [2158 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1 [13.7 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.18-1 [40.9 kB] Get:109 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4 [170 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.3 [107 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.3 [308 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-3 [323 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.3 [107 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.3 [120 kB] Get:115 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.1.0-1+b1 [520 kB] Get:116 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:117 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:118 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.2-6 [316 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6 [387 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1 [530 kB] Get:128 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.25.1-1 [112 kB] Get:129 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:130 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:131 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:132 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:134 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:135 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-2 [143 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.1-2 [807 kB] Get:137 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.1-2 [2185 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-1 [35.5 kB] Get:140 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20231126-1 [136 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-2 [64.6 kB] Get:142 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-2 [880 kB] Get:143 http://deb.debian.org/debian sid/main amd64 binutils-common amd64 2.41.50.20231206-1 [2537 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libsframe1 amd64 2.41.50.20231206-1 [75.2 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libbinutils amd64 2.41.50.20231206-1 [515 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.41.50.20231206-1 [151 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libctf0 amd64 2.41.50.20231206-1 [87.1 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.41.50.20231206-1 [768 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:150 http://deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.41.50.20231206-1 [2235 kB] Get:151 http://deb.debian.org/debian sid/main amd64 binutils amd64 2.41.50.20231206-1 [80.2 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libisl23 amd64 0.26-3 [700 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1 [713 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:155 http://deb.debian.org/debian sid/main amd64 cpp-13 amd64 13.2.0-8 [9915 kB] Get:156 http://deb.debian.org/debian sid/main amd64 cpp amd64 4:13.2.0-2 [7032 B] Get:157 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:159 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 13.2.0-8 [803 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.25+ds-1 [6640 kB] Get:162 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.58.0-1 [74.1 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-3 [214 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.5.0-1 [420 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.5.2-1 [90.2 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.18+ds-1 [441 kB] Get:169 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get:170 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libcc1-0 amd64 13.2.0-8 [43.0 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 13.2.0-8 [26.1 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 13.2.0-8 [9304 B] Get:174 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 13.2.0-8 [2558 kB] Get:175 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 13.2.0-8 [1102 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 13.2.0-8 [2334 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 13.2.0-8 [1010 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 13.2.0-8 [1154 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 13.2.0-8 [145 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-8 [2538 kB] Get:181 http://deb.debian.org/debian sid/main amd64 gcc-13 amd64 13.2.0-8 [19.6 MB] Get:182 http://deb.debian.org/debian sid/main amd64 gcc amd64 4:13.2.0-2 [5224 B] Get:183 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-13 [46.6 kB] Get:184 http://deb.debian.org/debian sid/main amd64 linux-libc-dev amd64 6.5.13-1 [2037 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-2 [118 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1 [188 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3 [66.9 kB] Get:188 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-13 [1902 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-8 [2227 kB] Get:191 http://deb.debian.org/debian sid/main amd64 g++-13 amd64 13.2.0-8 [10.9 MB] Get:192 http://deb.debian.org/debian sid/main amd64 g++ amd64 4:13.2.0-2 [1356 B] Get:193 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.25+ds-1 [36.8 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.25+ds-1 [4679 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.25+ds-1 [49.6 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libboost1.74-dev amd64 1.74.0+ds1-23+b1 [9509 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:198 http://deb.debian.org/debian sid/main amd64 libpython3.11 amd64 3.11.7-2 [1990 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libexpat1-dev amd64 2.5.0-2 [149 kB] Get:200 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3 [918 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libpython3.11-dev amd64 3.11.7-2 [4576 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.11.6-1 [9460 B] Get:203 http://deb.debian.org/debian sid/main amd64 libpython3.12 amd64 3.12.1-2 [2129 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libpython3.12-dev amd64 3.12.1-2 [4942 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libpython3-all-dev amd64 3.11.6-1 [1072 B] Get:206 http://deb.debian.org/debian sid/main amd64 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get:207 http://deb.debian.org/debian sid/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:208 http://deb.debian.org/debian sid/main amd64 python3-all amd64 3.11.6-1 [1060 B] Get:209 http://deb.debian.org/debian sid/main amd64 python3.11-dev amd64 3.11.7-2 [508 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-2 [149 kB] Get:213 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.11.6-1 [26.1 kB] Get:214 http://deb.debian.org/debian sid/main amd64 python3.12-dev amd64 3.12.1-2 [506 kB] Get:215 http://deb.debian.org/debian sid/main amd64 python3-all-dev amd64 3.11.6-1 [1076 B] Get:216 http://deb.debian.org/debian sid/main amd64 libxsimd-dev amd64 10.0.0-3 [101 kB] Get:217 http://deb.debian.org/debian sid/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:218 http://deb.debian.org/debian sid/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:219 http://deb.debian.org/debian sid/main amd64 python3-ply all 3.11-6 [63.7 kB] Get:220 http://deb.debian.org/debian sid/main amd64 python3-pythran amd64 0.14.0+ds-2 [440 kB] Get:221 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:222 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.10.1-6 [19.7 MB] Get:223 http://deb.debian.org/debian sid/main amd64 python3-joblib all 1.3.2-1 [217 kB] Get:224 http://deb.debian.org/debian sid/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:225 http://deb.debian.org/debian sid/main amd64 python3-sklearn-lib amd64 1.2.1+dfsg-1+b1 [4849 kB] Get:226 http://deb.debian.org/debian sid/main amd64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] Get:227 http://deb.debian.org/debian sid/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-10 [56.4 kB] Get:228 http://deb.debian.org/debian sid/main amd64 cutesv all 2.1.0-2 [36.9 kB] Get:229 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-12 [41.0 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4 [19.4 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4 [56.7 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 213 MB in 4s (55.6 MB/s) 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12281 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12281 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.5-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.4.5-0.1) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.4.5-0.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12281 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.7_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.7.7) over (2.6.1) ... Setting up libapt-pkg6.0:amd64 (2.7.7) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12276 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.9.0-4) ... Setting up findutils (4.9.0-5) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12275 files and directories currently installed.) Preparing to unpack .../libperl5.36_5.36.0-10_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-10) over (5.36.0-7+deb12u1) ... Preparing to unpack .../perl_5.36.0-10_amd64.deb ... Unpacking perl (5.36.0-10) over (5.36.0-7+deb12u1) ... Preparing to unpack .../perl-base_5.36.0-10_amd64.deb ... Unpacking perl-base (5.36.0-10) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.36.0-10) ... (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 ... 12275 files and directories currently installed.) Preparing to unpack .../perl-modules-5.36_5.36.0-10_all.deb ... Unpacking perl-modules-5.36 (5.36.0-10) over (5.36.0-7+deb12u1) ... Preparing to unpack .../libcrypt1_1%3a4.4.36-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-2) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12275 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libgdbm-compat4_1.23-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libblkid1_2.39.3-2_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-2) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12274 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-2_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-2) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12273 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-1_all.deb ... Unpacking libaudit-common (1:3.1.2-1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-1) ... (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 ... 12273 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-3_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.3-3) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.3-3) ... (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 ... 12272 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-1) ... (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 ... 12272 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-2) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12271 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-2_amd64.deb ... Unpacking util-linux-extra (2.39.3-2) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty Setting up util-linux-extra (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12276 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-2_amd64.deb ... Unpacking util-linux (2.39.3-2) over (2.38.1-5+b1) ... Setting up util-linux (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12278 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libnettle8:amd64 (3.9.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12278 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-2) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12278 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-2) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.3-2) ... Selecting previously unselected package libunistring5: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 ... 12278 files and directories currently installed.) Preparing to unpack .../libunistring5_1.1-2_amd64.deb ... Unpacking libunistring5:amd64 (1.1-2) ... Setting up libunistring5:amd64 (1.1-2) ... (Reading database ... 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Unpacking python3-sklearn (1.2.1+dfsg-1) ... Preparing to unpack .../87-python3-vcf_0.6.8+git20170215.476169c-10_amd64.deb ... Unpacking python3-vcf (0.6.8+git20170215.476169c-10) over (0.6.8+git20170215.476169c-9+b1) ... Preparing to unpack .../88-cutesv_2.1.0-2_all.deb ... Unpacking cutesv (2.1.0-2) over (2.0.2-1) ... Preparing to unpack .../89-gcc-12-base_12.3.0-12_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-12) over (12.2.0-14) ... Preparing to unpack .../90-libbsd0_0.11.7-4_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-4) over (0.11.7-2) ... Preparing to unpack .../91-libsasl2-modules-db_2.1.28+dfsg1-4_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4) over (2.1.28+dfsg-10) ... Preparing to unpack .../92-libsasl2-2_2.1.28+dfsg1-4_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4) over (2.1.28+dfsg-10) ... Preparing to unpack .../93-libss2_1.47.0-2+b1_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2+b1) over (1.47.0-2) ... Setting up libhtscodecs2:amd64 (1.5.2-1) ... Setting up media-types (10.1.0) ... Installing new version of config file /etc/mime.types ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libsharpyuv0:amd64 (1.3.2-0.3) ... Setting up libpsl5:amd64 (0.21.2-1+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libglib2.0-0:amd64 (2.78.3-1) ... No schema files found: doing nothing. Setting up fontconfig-config (2.14.2-6) ... Setting up libtirpc-common (1.3.4+ds-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b1) ... Setting up libsqlite3-0:amd64 (3.44.2-1) ... Setting up libpython3.12-minimal:amd64 (3.12.1-2) ... Setting up binutils-common:amd64 (2.41.50.20231206-1) ... Setting up libnghttp2-14:amd64 (1.58.0-1) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up linux-libc-dev:amd64 (6.5.13-1) ... Setting up libctf-nobfd0:amd64 (2.41.50.20231206-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libgomp1:amd64 (13.2.0-8) ... Setting up libsframe1:amd64 (2.41.50.20231206-1) ... Setting up libjansson4:amd64 (2.14-2) ... Setting up libkrb5support0:amd64 (1.20.1-5) ... Setting up gcc-12-base:amd64 (12.3.0-12) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4) ... Setting up tzdata (2023c-11) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Dec 11 21:26:06 UTC 2023. Universal Time is now: Mon Dec 11 21:26:06 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxsimd-dev:amd64 (10.0.0-3) ... Setting up perl-modules-5.36 (5.36.0-10) ... Setting up rpcsvc-proto (1.4.3-1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libmpfr6:amd64 (4.2.1-1) ... Setting up libfribidi0:amd64 (1.0.13-3) ... Setting up libquadmath0:amd64 (13.2.0-8) ... Setting up libimagequant0:amd64 (2.18.0-1) ... Setting up libproc2-0:amd64 (2:4.0.4-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.40-2) ... Setting up libmpc3:amd64 (1.3.1-1) ... Setting up libatomic1:amd64 (13.2.0-8) ... Setting up libss2:amd64 (1.47.0-2+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.4+20231121-1) ... Setting up libk5crypto3:amd64 (1.20.1-5) ... Setting up logsave (1.47.0-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4) ... Setting up libgfortran5:amd64 (13.2.0-8) ... Setting up libwebp7:amd64 (1.3.2-0.3) ... Setting up libubsan1:amd64 (13.2.0-8) ... Setting up fonts-dejavu-extra (2.37-8) ... Setting up mount (2.39.3-2) ... Setting up libhwasan0:amd64 (13.2.0-8) ... Setting up libcrypt-dev:amd64 (1:4.4.36-2) ... Setting up libtiff6:amd64 (4.5.1+git230720-3) ... Setting up libasan8:amd64 (13.2.0-8) ... Setting up procps (2:4.0.4-2) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libssh2-1:amd64 (1.11.0-3) ... Setting up netbase (6.4) ... Setting up mawk (1.3.4.20231126-1) ... Setting up libkrb5-3:amd64 (1.20.1-5) ... Setting up libtsan2:amd64 (13.2.0-8) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.41.50.20231206-1) ... Setting up libisl23:amd64 (0.26-3) ... Setting up libc-dev-bin (2.37-13) ... Setting up libwebpmux3:amd64 (1.3.2-0.3) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up readline-common (8.2-3) ... Setting up libcc1-0:amd64 (13.2.0-8) ... Setting up liblsan0:amd64 (13.2.0-8) ... Setting up libitm1:amd64 (13.2.0-8) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libctf0:amd64 (2.41.50.20231206-1) ... Setting up python3.12-minimal (3.12.1-2) ... Setting up libopenblas0-pthread:amd64 (0.3.25+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up cpp-13 (13.2.0-8) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.3) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up e2fsprogs (1.47.0-2+b1) ... Setting up libgprofng0:amd64 (2.41.50.20231206-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libjs-sphinxdoc (7.2.6-2) ... Setting up libgcc-13-dev:amd64 (13.2.0-8) ... Setting up libopenblas0:amd64 (0.3.25+ds-1) ... Setting up cpp (4:13.2.0-2) ... Setting up libharfbuzz0b:amd64 (8.0.1-1) ... Setting up libperl5.36:amd64 (5.36.0-10) ... Setting up binutils-x86-64-linux-gnu (2.41.50.20231206-1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.25+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libcurl3-gnutls:amd64 (8.5.0-1) ... Setting up binutils (2.41.50.20231206-1) ... Setting up libopenblas-dev:amd64 (0.3.25+ds-1) ... Setting up perl (5.36.0-10) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1) ... Setting up libraqm0:amd64 (0.10.1-1) ... Setting up gcc-13 (13.2.0-8) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libhts3:amd64 (1.18+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.1-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up gcc (4:13.2.0-2) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up libc6-dev:amd64 (2.37-13) ... Setting up libpython3.12:amd64 (3.12.1-2) ... Setting up libstdc++-13-dev:amd64 (13.2.0-8) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up g++-13 (13.2.0-8) ... Setting up python3.11 (3.11.7-2) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-23+b1) ... Setting up libpython3.11:amd64 (3.11.7-2) ... Setting up python3 (3.11.6-1) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-pil:amd64 (10.1.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up libexpat1-dev:amd64 (2.5.0-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3) ... Setting up g++ (4:13.2.0-2) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up python3-joblib (1.3.2-1) ... Setting up python3-ply (3.11-6) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.1-2) ... Setting up python3-vcf (0.6.8+git20170215.476169c-10) ... /usr/lib/python3/dist-packages/vcf/parser.py:278: SyntaxWarning: invalid escape sequence '\[' self._alt_pattern = re.compile('[\[\]]') /usr/lib/python3/dist-packages/vcf/parser.py:536: SyntaxWarning: invalid escape sequence '\[' remoteOrientation = (re.search('\[', str) is not None) Setting up python3-beniget (0.4.1-3) ... Setting up libpython3.11-dev:amd64 (3.11.7-2) ... Setting up python3.12-dev (3.12.1-2) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up libpython3-dev:amd64 (3.11.6-1) ... Setting up python3.11-dev (3.11.7-2) ... Setting up python3-sklearn-lib:amd64 (1.2.1+dfsg-1+b1) ... Setting up libpython3-all-dev:amd64 (3.11.6-1) ... Setting up python3-dev (3.11.6-1) ... Setting up python3-all-dev (3.11.6-1) ... Setting up python3-pythran (0.14.0+ds-2) ... Setting up python3-scipy (1.10.1-6) ... Setting up python3-sklearn (1.2.1+dfsg-1) ... Processing triggers for sgml-base (1.31) ... Processing triggers for debianutils (5.14) ... Setting up libfontconfig1:amd64 (2.14.2-6) ... Processing triggers for mailcap (3.70+nmu1) ... Processing triggers for libc-bin (2.37-13) ... Setting up libcairo2:amd64 (1.18.0-1) ... Setting up python3-cairo:amd64 (1.25.1-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.0.7-1) ... Setting up python3-biopython (1.81+dfsg-2+b1) ... Setting up cutesv (2.1.0-2) ... Processing triggers for libc-bin (2.37-13) ... 2m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-yf', 'dist-upgrade'] 2m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m43.0s DUMP: ea7d3452d56f82a51a1482aee283bdb2 - 2m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'show', '--no-all-versions', 'cutesv'] 2m43.3s DUMP: Package: cutesv Version: 2.1.0-2 Installed-Size: 222 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-cigar, python3-numpy, python3-pysam, python3-scipy, python3-sklearn, python3-vcf, python3:any 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_2.1.0-2_all.deb Size: 36872 MD5sum: 151d9c85cee35c8ad2cc29047ee88d8d SHA256: a2763c15d8db22f795aa5739351fe04959c5045e26cd06bdbb6610558a4c0777 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'show', '--no-all-versions', 'cutesv'] 2m43.3s INFO: apt-cache knows about the following packages: cutesv 2m43.3s INFO: Running scripts pre_install 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 2m43.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 2m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 2m43.5s DUMP: cutesv: Installed: 2.1.0-2 Candidate: 2.1.0-2 Version table: *** 2.1.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 2m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv'] 2m44.1s DUMP: Reading package lists... Building dependency tree... Reading state information... cutesv is already the newest version (2.1.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv'] 2m44.1s INFO: Running scripts post_install 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 2m44.1s INFO: Running scripts post_distupgrade 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_exceptions'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_exceptions'] 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_zz_backports'] 2m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_distupgrade_zz_backports'] 2m44.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m45.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m45.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m46.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m46.9s INFO: Running scripts pre_install 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_database-server'] 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_exceptions'] 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_extras'] 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture'] 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m46.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 2m47.0s 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: 2m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy'] 2m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 2m47.1s DUMP: cutesv: Installed: 2.1.0-2 Candidate: 2.1.0-2 Version table: *** 2.1.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-cache', 'policy', 'cutesv'] 2m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv=2.1.0-2'] 2m47.7s DUMP: Reading package lists... Building dependency tree... Reading state information... cutesv is already the newest version (2.1.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m47.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', '-y', 'install', 'cutesv=2.1.0-2'] 2m47.7s INFO: Running scripts post_install 2m47.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 2m47.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_install_exceptions'] 2m47.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m49.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 2m49.1s INFO: /bin converted to /usr/bin by /usr merge 2m49.1s INFO: /lib converted to /usr/lib by /usr merge 2m49.1s INFO: /lib/init converted to /usr/lib/init by /usr merge 2m49.1s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 2m49.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 2m49.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m49.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m49.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m49.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m49.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m49.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 2m49.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m49.1s INFO: /sbin converted to /usr/sbin by /usr merge 2m51.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', '-ac', '--ignore-obsolete'] 2m56.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', '-ac', '--ignore-obsolete'] 2m56.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m56.5s DUMP: 0.15.6 2m56.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m56.5s INFO: Running adequate version 0.15.6 now. 2m56.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'cutesv'] 2m56.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'cutesv'] 2m56.6s INFO: Running scripts pre_remove 2m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_exceptions'] 3m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/pre_remove_exceptions'] 3m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m4.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.7 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed binutils binutils 2.41.50.20231206-1 install ok installed binutils-common:amd64 binutils-common 2.41.50.20231206-1 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.41.50.20231206-1 install ok installed bsdutils bsdutils 1:2.39.3-2 install ok installed coreutils coreutils 9.4-2+b1 install ok installed cpp cpp 4:13.2.0-2 install ok installed cpp-13 cpp-13 13.2.0-8 install ok installed cutesv cutesv 2.1.0-2 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.14 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.1 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig-config fontconfig-config 2.14.2-6 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed g++ g++ 4:13.2.0-2 install ok installed g++-13 g++-13 13.2.0-8 install ok installed gcc gcc 4:13.2.0-2 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-12 install ok installed gcc-13 gcc-13 13.2.0-8 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-8 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.7 install ok installed libasan8:amd64 libasan8 13.2.0-8 install ok installed libatomic1:amd64 libatomic1 13.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libbinutils:amd64 libbinutils 2.41.50.20231206-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-2 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-23+b1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b1 install ok installed libbsd0:amd64 libbsd0 0.11.7-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-13 install ok installed libc-dev-bin libc-dev-bin 2.37-13 install ok installed libc6:amd64 libc6 2.37-13 install ok installed libc6-dev:amd64 libc6-dev 2.37-13 install ok installed libcairo2:amd64 libcairo2 1.18.0-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcc1-0:amd64 libcc1-0 13.2.0-8 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.41.50.20231206-1 install ok installed libctf0:amd64 libctf0 2.41.50.20231206-1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.5.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.18-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-2 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.5.0-2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.2-6 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-8 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5 install ok installed libgdbm6:amd64 libgdbm6 1.23-5 install ok installed libgfortran5:amd64 libgfortran5 13.2.0-8 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.3-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.2-1 install ok installed libgomp1:amd64 libgomp1 13.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgprofng0:amd64 libgprofng0 2.41.50.20231206-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.0.1-1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.18+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.5.2-1 install ok installed libhwasan0:amd64 libhwasan0 13.2.0-8 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libisl23:amd64 libisl23 0.26-3 install ok installed libitm1:amd64 libitm1 13.2.0-8 install ok installed libjansson4:amd64 libjansson4 2.14-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-2 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4 install ok installed liblsan0:amd64 liblsan0 13.2.0-8 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.3-2 install ok installed libmpc3:amd64 libmpc3 1.3.1-1 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20231121-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.58.0-1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.25+ds-1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.25+ds-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.25+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.25+ds-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-10 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.40-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-2 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.6-1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.6-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11:amd64 libpython3.11 3.11.7-2 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.7-2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.7-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.7-2 install ok installed libpython3.12:amd64 libpython3.12 3.12.1-2 install ok installed libpython3.12-dev:amd64 libpython3.12-dev 3.12.1-2 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.1-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.1-2 install ok installed libquadmath0:amd64 libquadmath0 13.2.0-8 install ok installed libraqm0:amd64 libraqm0 0.10.1-1 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-2+b1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsframe1:amd64 libsframe1 2.41.50.20231206-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.3 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.44.2-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-3 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 255-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20231121-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtsan2:amd64 libtsan2 13.2.0-8 install ok installed libubsan1:amd64 libubsan1 13.2.0-8 install ok installed libudev1:amd64 libudev1 255-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.3 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.3.2-0.3 install ok installed libwebpmux3:amd64 libwebpmux3 1.3.2-0.3 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxsimd-dev:amd64 libxsimd-dev 10.0.0-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.5.13-1 install ok installed login login 1:4.13+dfsg1-3 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed media-types media-types 10.1.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.39.3-2 install ok installed ncurses-base ncurses-base 6.4+20231121-1 install ok installed ncurses-bin ncurses-bin 6.4+20231121-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-3 install ok installed perl perl 5.36.0-10 install ok installed perl-base perl-base 5.36.0-10 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-10 install ok installed procps procps 2:4.0.4-2 install ok installed python3 python3 3.11.6-1 install ok installed python3-all python3-all 3.11.6-1 install ok installed python3-all-dev python3-all-dev 3.11.6-1 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-biopython python3-biopython 1.81+dfsg-2+b1 install ok installed python3-cairo:amd64 python3-cairo 1.25.1-1 install ok installed python3-cigar python3-cigar 0.1.3-2 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dev python3-dev 3.11.6-1 install ok installed python3-distutils python3-distutils 3.11.5-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-joblib python3-joblib 1.3.2-1 install ok installed python3-lib2to3 python3-lib2to3 3.11.5-1 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-pil:amd64 python3-pil 10.1.0-1+b1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-ply python3-ply 3.11-6 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b1 install ok installed python3-pythran python3-pythran 0.14.0+ds-2 install ok installed python3-reportlab python3-reportlab 4.0.7-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.10.1-6 install ok installed python3-sklearn python3-sklearn 1.2.1+dfsg-1 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 1.2.1+dfsg-1+b1 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-vcf python3-vcf 0.6.8+git20170215.476169c-10 install ok installed python3.11 python3.11 3.11.7-2 install ok installed python3.11-dev python3.11-dev 3.11.7-2 install ok installed python3.11-minimal python3.11-minimal 3.11.7-2 install ok installed python3.12 python3.12 3.12.1-2 install ok installed python3.12-dev python3.12-dev 3.12.1-2 install ok installed python3.12-minimal python3.12-minimal 3.12.1-2 install ok installed readline-common readline-common 8.2-3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-1 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-11 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.3-2 install ok installed util-linux-extra util-linux-extra 2.39.3-2 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3 3m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'cpp', 'cpp-13', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++-', 'g++-13', 'gcc', 'gcc-13', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-13-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'procps', 'python3', 'python3-all', 'python3-all-dev', 'python3-beniget', 'python3-biopython', 'python3-cairo:amd64', 'python3-cigar', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-freetype', 'python3-gast', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64', 'cutesv'] 3m59.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-13 cutesv fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 g++ g++-13 gcc gcc-13 libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libdeflate0 libexpat1 libexpat1-dev libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-13-dev libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libhwasan0 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 liblsan0 libmpc3 libmpfr6 libncursesw6 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.36 libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsframe1 libsharpyuv0 libsqlite3-0 libssh2-1 libstdc++-13-dev libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 libxsimd-dev linux-libc-dev mailcap media-types mime-support netbase perl perl-modules-5.36 procps python3 python3-all python3-all-dev python3-beniget python3-biopython python3-cairo python3-cigar python3-decorator python3-dev python3-distutils python3-freetype python3-gast python3-joblib python3-lib2to3 python3-minimal python3-numpy python3-pil python3-pkg-resources python3-ply python3-pysam python3-pythran python3-reportlab python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-vcf python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal readline-common rpcsvc-proto sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 0 newly installed, 178 to remove and 0 not upgraded. After this operation, 1002 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 ... 37802 files and directories currently installed.) Removing cutesv (2.1.0-2) ... Removing python3-sklearn (1.2.1+dfsg-1) ... Removing python3-scipy (1.10.1-6) ... Removing python3-pythran (0.14.0+ds-2) ... Removing g++ (4:13.2.0-2) ... Removing gcc (4:13.2.0-2) ... Removing cpp (4:13.2.0-2) ... Removing python3-biopython (1.81+dfsg-2+b1) ... Removing python3-reportlab (4.0.7-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo:amd64 (1.25.1-1) ... Removing libcairo2:amd64 (1.18.0-1) ... Removing libfontconfig1:amd64 (2.14.2-6) ... Removing fontconfig-config (2.14.2-6) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-urw-base35 (20200910-7) ... Removing g++-13 (13.2.0-8) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0+ds1-23+b1) ... Removing libstdc++-13-dev:amd64 (13.2.0-8) ... Removing python3-sklearn-lib:amd64 (1.2.1+dfsg-1+b1) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-pil:amd64 (10.1.0-1+b1) ... Removing libraqm0:amd64 (0.10.1-1) ... Removing python3-vcf (0.6.8+git20170215.476169c-10) ... Removing python3-pysam (0.22.0+ds-1+b1) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.5.0-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing python3-all-dev (3.11.6-1) ... Removing python3.12-dev (3.12.1-2) ... Removing libpython3-all-dev:amd64 (3.11.6-1) ... Removing libpython3.12-dev:amd64 (3.12.1-2) ... Removing python3-dev (3.11.6-1) ... Removing python3.11-dev (3.11.7-2) ... Removing libtiff6:amd64 (4.5.1+git230720-3) ... Removing libdeflate0:amd64 (1.18-1) ... Removing python3-all (3.11.6-1) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing libpython3.12:amd64 (3.12.1-2) ... Removing libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.13-3) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing python3-distutils (3.11.5-1) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.36.0-10) ... Removing libperl5.36:amd64 (5.36.0-10) ... Removing libgdbm-compat4:amd64 (1.23-5) ... Removing libgdbm6:amd64 (1.23-5) ... Removing libopenblas-dev:amd64 (0.3.25+ds-1) ... Removing libopenblas-pthread-dev:amd64 (0.3.25+ds-1) ... Removing libopenblas0:amd64 (0.3.25+ds-1) ... Removing libopenblas0-pthread:amd64 (0.3.25+ds-1) ... Removing libgfortran5:amd64 (13.2.0-8) ... Removing libharfbuzz0b:amd64 (8.0.1-1) ... Removing libglib2.0-0:amd64 (2.78.3-1) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libhtscodecs2:amd64 (1.5.2-1) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libjs-sphinxdoc (7.2.6-2) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-4) ... Removing python3-joblib (1.3.2-1) ... Removing procps (2:4.0.4-2) ... Removing libnghttp2-14:amd64 (1.58.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libproc2-0:amd64 (2:4.0.4-2) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3-dev:amd64 (3.11.6-1) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4) ... Removing libwebpmux3:amd64 (1.3.2-0.3) ... Removing libwebpdemux2:amd64 (1.3.2-0.3) ... Removing libwebp7:amd64 (1.3.2-0.3) ... Removing libsharpyuv0:amd64 (1.3.2-0.3) ... Removing libssh2-1:amd64 (1.11.0-3) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxsimd-dev:amd64 (10.0.0-3) ... Removing perl-modules-5.36 (5.36.0-10) ... Removing python3-beniget (0.4.1-3) ... Removing python3-cigar (0.1.3-2) ... Removing python3-decorator (5.1.1-5) ... Removing python3-freetype (2.4.0-1) ... Removing python3-gast (0.5.2-2) ... Removing python3-lib2to3 (3.11.5-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-ply (3.11-6) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing gcc-13 (13.2.0-8) ... Removing binutils (2.41.50.20231206-1) ... Removing binutils-x86-64-linux-gnu (2.41.50.20231206-1) ... Removing libgprofng0:amd64 (2.41.50.20231206-1) ... Removing libctf0:amd64 (2.41.50.20231206-1) ... Removing libbinutils:amd64 (2.41.50.20231206-1) ... Removing binutils-common:amd64 (2.41.50.20231206-1) ... Removing cpp-13 (13.2.0-8) ... Removing libgcc-13-dev:amd64 (13.2.0-8) ... Removing libasan8:amd64 (13.2.0-8) ... Removing libatomic1:amd64 (13.2.0-8) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b1) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-4) ... Removing libpython3.11-dev:amd64 (3.11.7-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3) ... Removing libexpat1-dev:amd64 (2.5.0-2) ... Removing libc6-dev:amd64 (2.37-13) ... Removing libc-dev-bin (2.37-13) ... Removing libcc1-0:amd64 (13.2.0-8) ... Removing libcrypt-dev:amd64 (1:4.4.36-2) ... Removing libctf-nobfd0:amd64 (2.41.50.20231206-1) ... Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.7-2) ... Removing libgomp1:amd64 (13.2.0-8) ... Removing libpython3.11:amd64 (3.11.7-2) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl-dev:amd64 (1.3.0-3) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1) ... Removing libhwasan0:amd64 (13.2.0-8) ... Removing libisl23:amd64 (0.26-3) ... Removing libitm1:amd64 (13.2.0-8) ... Removing libjansson4:amd64 (2.14-2) ... Removing liblsan0:amd64 (13.2.0-8) ... Removing libmpc3:amd64 (1.3.1-1) ... Removing libmpfr6:amd64 (4.2.1-1) ... Removing libncursesw6:amd64 (6.4+20231121-1) ... Removing libnsl2:amd64 (1.3.0-3) ... Removing libpng16-16:amd64 (1.6.40-2) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.7-2) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (13.2.0-8) ... Removing libreadline8:amd64 (8.2-3) ... Removing libsframe1:amd64 (2.41.50.20231206-1) ... Removing libsqlite3-0:amd64 (3.44.2-1) ... Removing libtsan2:amd64 (13.2.0-8) ... Removing libubsan1:amd64 (13.2.0-8) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing linux-libc-dev:amd64 (6.5.13-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Removing rpcsvc-proto (1.4.3-1) ... Removing libexpat1:amd64 (2.5.0-2) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libtirpc-common (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-13) ... 3m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'cpp', 'cpp-13', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++-', 'g++-13', 'gcc', 'gcc-13', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-13-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'procps', 'python3', 'python3-all', 'python3-all-dev', 'python3-beniget', 'python3-biopython', 'python3-cairo:amd64', 'python3-cigar', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-freetype', 'python3-gast', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64', 'cutesv'] 3m59.9s INFO: Running scripts post_remove 3m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_remove_exceptions'] 3m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_remove_exceptions'] 3m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'cpp', 'cpp-13', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++', 'g++-13', 'gcc', 'gcc-13', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-13-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'procps', 'python3', 'python3-all', 'python3-all-dev', 'python3-beniget', 'python3-biopython', 'python3-cairo:amd64', 'python3-cigar', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-freetype', 'python3-gast', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64'] 4m0.6s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 5395 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.41.50.20231206-1) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove cpp which isn't installed dpkg: warning: ignoring request to remove cpp-13 which isn't installed Purging configuration files for fontconfig-config (2.14.2-6) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... dpkg: warning: ignoring request to remove fonts-dejavu-extra which isn't installed Purging configuration files for fonts-dejavu-mono (2.37-8) ... Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-13 which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-13 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.74-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-2) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libcurl3-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 libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-13-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.3-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-all-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.11 which isn't installed dpkg: warning: ignoring request to remove libpython3.11-dev which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.7-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12 which isn't installed dpkg: warning: ignoring request to remove libpython3.12-dev which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.1-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 libsframe1 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-dev which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove 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 dpkg: warning: ignoring request to remove libxsimd-dev which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for netbase (6.4) ... Purging configuration files for perl (5.36.0-10) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for procps (2:4.0.4-2) ... Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-all which isn't installed dpkg: warning: ignoring request to remove python3-all-dev which isn't installed dpkg: warning: ignoring request to remove python3-beniget which isn't installed 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-cigar which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dev which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-gast which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-ply which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-pythran 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 python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.7-2) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed dpkg: warning: ignoring request to remove python3.12-dev which isn't installed Purging configuration files for python3.12-minimal (3.12.1-2) ... Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed 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+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 4m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'cpp', 'cpp-13', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'g++', 'g++-13', 'gcc', 'gcc-13', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-13-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-13-dev:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxsimd-dev:amd64', 'linux-libc-dev:amd64', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'procps', 'python3', 'python3-all', 'python3-all-dev', 'python3-beniget', 'python3-biopython', 'python3-cairo:amd64', 'python3-cigar', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-freetype', 'python3-gast', 'python3-joblib', 'python3-lib2to3', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-vcf', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'zlib1g-dev:amd64'] 4m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', 'cutesv'] 4m0.6s DUMP: dpkg: warning: ignoring request to remove cutesv which isn't installed 4m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', 'cutesv'] 4m0.6s INFO: Running scripts post_purge 4m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_purge_exceptions'] 4m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_purge_exceptions'] 4m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', '--pending'] 4m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--purge', '--pending'] 4m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--remove', '--pending'] 4m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg', '--remove', '--pending'] 4m0.7s INFO: Running scripts post_test 4m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_test_exceptions'] 4m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'tmp/scripts/post_test_exceptions'] 4m0.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 4m1.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 4m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-divert', '--list'] 4m1.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 4m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'dpkg-divert', '--list'] 4m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'clean'] 4m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04', 'apt-get', 'clean'] 4m1.1s DEBUG: Recording chroot state 4m1.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/shm'] 4m1.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/shm'] 4m1.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/console'] 4m1.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/console'] 4m1.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/ptmx'] 4m1.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/ptmx'] 4m1.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts'] 4m1.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/dev/pts'] 4m1.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/proc'] 4m2.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04/proc'] 4m2.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 4m2.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcyt5xo04'] 4m2.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpcyt5xo04 4m2.1s INFO: PASS: Upgrading between Debian distributions. 4m2.1s INFO: PASS: All tests. 4m2.1s INFO: piuparts run ends. ret=0 End: 2023-12-11 21:27:58 GMT