Start: 2024-02-04 15:44:10 GMT [testing] Package: python3-nanoget Source: python-nanoget Version: 1.16.1-2 Installed-Size: 51 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-numpy, python3-pandas, python3-pysam, python3:any, python3-nanomath Description: extract information from Oxford Nanopore sequencing data and alignments Homepage: https://github.com/wdecoster/nanoget Description-md5: b717656953ba87a065e49966061c1863 Section: python Priority: optional Filename: pool/main/p/python-nanoget/python3-nanoget_1.16.1-2_all.deb Size: 11392 MD5sum: 6c466e8eea8727123a21a1c06876cfa0 SHA256: 5510935625e436152313ef546b9b47f509774d5739ceb7b260ffbdff55bc9ead [sid] Package: python3-nanoget Source: python-nanoget Version: 1.19.3-1 Installed-Size: 52 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-numpy, python3-pandas (>= 2.0.0), python3-pysam, python3:any, python3-nanomath Description: extract information from Oxford Nanopore sequencing data and alignments Homepage: https://github.com/wdecoster/nanoget Description-md5: b717656953ba87a065e49966061c1863 Section: python Priority: optional Filename: pool/main/p/python-nanoget/python3-nanoget_1.19.3-1_all.deb Size: 11700 MD5sum: b27c8749ed1dec14ef9ed4d10ff99a5f SHA256: a69909d14fdd8d5ed3137c6a6864ab1562467bf49c44d37b55cfac7d65735510 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 python3-nanoget=1.19.3-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311821~1.3-2-g28295102 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 python3-nanoget=1.19.3-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpmcu_70iy 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmcu_70iy 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpmcu_70iy/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'update'] 0m3.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'update'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s INFO: Running scripts post_setup 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s 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' 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_minimize'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_setup_zz_backports'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s 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 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 0m5.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 0m5.6s INFO: Running scripts is_testable 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s INFO: Running scripts pre_test 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_test_root_password'] 0m5.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_test_root_password'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'show', '--no-all-versions', 'python3-nanoget'] 0m5.9s DUMP: Package: python3-nanoget Source: python-nanoget Version: 1.16.1-2 Installed-Size: 51 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-numpy, python3-pandas, python3-pysam, python3:any, python3-nanomath Description-en: extract information from Oxford Nanopore sequencing data and alignments The Python3 module nanoget provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments. . Data can be presented in the following formats, using the following functions: . * sorted bam file process_bam(bamfile, threads) * standard fastq file process_fastq_plain(fastqfile, 'threads') * fastq file with metadata from MinKNOW or Albacore process_fastq_rich(fastqfile) * sequencing_summary file generated by Albacore process_summary(sequencing_summary.txt, 'readtype') . Fastq files can be compressed using gzip, bzip2 or bgzip. The data is returned as a pandas DataFrame with standardized headernames for convenient extraction. The functions perform logging while being called and extracting data. Description-md5: b717656953ba87a065e49966061c1863 Homepage: https://github.com/wdecoster/nanoget Section: python Priority: optional Filename: pool/main/p/python-nanoget/python3-nanoget_1.16.1-2_all.deb Size: 11392 MD5sum: 6c466e8eea8727123a21a1c06876cfa0 SHA256: 5510935625e436152313ef546b9b47f509774d5739ceb7b260ffbdff55bc9ead 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'show', '--no-all-versions', 'python3-nanoget'] 0m5.9s INFO: apt-cache knows about the following packages: python3-nanoget 0m5.9s INFO: Running scripts pre_install 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 0m6.0s 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: 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 0m6.0s DUMP: python3-nanoget: Installed: (none) Candidate: 1.16.1-2 Version table: 1.16.1-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget'] 1m12.5s DUMP: Reading package lists... Building dependency tree... 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-dateutil python3-deprecated python3-minimal python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-six python3-tz python3-wrapt 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-pandas-doc python3-statsmodels 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-scipy python3-matplotlib python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba python3-olefile The following NEW 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-dateutil python3-deprecated python3-minimal python3-nanoget python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-six python3-tz python3-wrapt python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 56.8 MB of archives. After this operation, 225 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian 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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libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:43 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amd64 2.14-2 [154 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.14.1-2+b2 [42.1 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 python3-deprecated all 1.2.13-3 [14.1 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 python3-nanomath all 1.2.1+ds-1 [8120 B] Get:92 http://deb.debian.org/debian bookworm/main amd64 python3-nanoget all 1.16.1-2 [11.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.8 MB in 0s (135 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-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... 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-wrapt (1.14.1-2+b2) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-deprecated (1.2.13-3) ... 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-numpy (1:1.24.2-1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-nanomath (1.2.1+ds-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 python3-nanoget (1.16.1-2) ... 1m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget'] 1m12.5s INFO: Running scripts post_install 1m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 1m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 1m12.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 1m13.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 1m13.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpmcu_70iy to sid 1m13.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m13.6s INFO: Running scripts pre_distupgrade 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_exceptions'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_exceptions'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'update'] 1m18.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9714 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7130 kB] Fetched 17.0 MB in 3s (5037 kB/s) Reading package lists... 1m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'update'] 1m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-yf', 'dist-upgrade'] 2m10.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: python3-renderpm python3-reportlab-accel The following NEW packages will be installed: fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono gcc-14-base libcairo2 libfontconfig1 libperl5.38 libpixman-1-0 libpython3.12-minimal libpython3.12-stdlib libsharpyuv0 libunistring5 libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxext6 libxrender1 netbase perl-modules-5.38 python3-cairo python3-chardet python3-freetype python3-rlpycairo python3.12 python3.12-minimal The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base gpgv grep hostname init-system-helpers libacl1 libapt-pkg6.0 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcom-err2 libcrypt1 libcurl3-gnutls libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libffi8 libfontenc1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libhtscodecs2 libidn2-0 libimagequant0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblz4-1 liblzma5 libmd0 libmount1 libncursesw6 libnettle8 libnghttp2-14 libnsl2 libopenjp2-7 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 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 python3 python3-biopython python3-dateutil python3-deprecated python3-minimal python3-nanoget python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-tz python3-wrapt python3.11 python3.11-minimal readline-common sed sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra xml-core zlib1g 158 upgraded, 27 newly installed, 2 to remove and 0 not upgraded. Need to get 97.8 MB of archives. After this operation, 168 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 5.16 [88.9 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 1:2.39.3-6 [96.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15 [2750 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240201-3 [42.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240201-3 [71.6 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 9.4-3+b1 [2950 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 14-20240201-3 [714 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-4+b2 [27.6 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-2 [362 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-2 [124 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:22 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.10 [982 kB] Get:24 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:25 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:26 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:27 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:28 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:29 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:30 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:31 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3+b1 [616 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:34 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:35 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:37 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:38 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:43 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6 [159 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6 [190 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2 [11.3 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-1 [16.9 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2 [48.4 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6 [117 kB] Get:52 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-6 [155 kB] Get:53 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-6 [1230 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:63 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:64 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.85 [119 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1+b1 [65.8 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:67 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1+b1 [50.1 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1+b1 [265 kB] Get:71 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3+b1 [973 kB] Get:72 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:73 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:74 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:76 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.10 [1363 kB] Get:77 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] Get:78 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:79 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:80 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-6 [32.1 kB] Get:81 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.81+dfsg-3 [1625 kB] Get:82 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.0.9-1 [674 kB] Get:83 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:84 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:85 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:86 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2+b2 [9140 B] Get:94 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:97 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-6 [29.7 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-nanoget all 1.19.3-1 [11.7 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.1.4+dfsg-3 [3015 kB] Get:107 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.1-2 [807 kB] Get:111 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.1-2 [2185 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:113 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-2 [148 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240201-3 [836 kB] Get:116 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-2 [2407 kB] Get:117 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-1 [421 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1 [92.8 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.18+ds-1 [441 kB] Get:129 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get:130 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.8.2-3 [78.4 kB] Get:131 http://deb.debian.org/debian sid/main amd64 python3-tz all 2023.4-1 [30.8 kB] Get:132 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-3 [7884 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:134 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240201-3 [136 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b2 [190 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-2 [1452 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1 [13.7 kB] Get:146 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4 [170 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.3 [107 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.3 [308 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.3 [107 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.3 [120 kB] Get:152 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.2.0-1 [525 kB] Get:153 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:154 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:155 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.2-6+b1 [316 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6+b1 [388 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:165 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.25.1-2 [140 kB] Get:166 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:167 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:168 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:169 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:171 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:172 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6 [143 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:177 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240201-3 [147 kB] Get:179 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-14 [41.2 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.8-1 [125 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1+b2 [23.3 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:183 http://deb.debian.org/debian sid/main amd64 python3-wrapt amd64 1.15.0-2+b1 [49.3 kB] Get:184 http://deb.debian.org/debian sid/main amd64 python3-deprecated all 1.2.14-1 [14.3 kB] Get:185 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 97.8 MB in 1s (95.0 MB/s) (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 ... 14054 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.10_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.7.10) over (2.6.1) ... Setting up libapt-pkg6.0:amd64 (2.7.10) ... (Reading database ... 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Unpacking libperl5.38:amd64 (5.38.2-3) ... Preparing to unpack .../perl-base_5.38.2-3_amd64.deb ... Unpacking perl-base (5.38.2-3) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-3) ... (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 ... 15979 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (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 ... 15976 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-6_amd64.deb ... Unpacking util-linux-extra (2.39.3-6) 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 (2.39.3-6) ... (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 ... 15983 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 ... 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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 ... 15989 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.3-1+b1) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (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 ... 15990 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.8.3-1_amd64.deb ... Unpacking libgnutls30:amd64 (3.8.3-1) over (3.7.9-2+deb12u1) ... Setting up libgnutls30:amd64 (3.8.3-1) ... (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 ... 15989 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271) over (0.270) ... Setting up libdebconfclient0:amd64 (0.271) ... (Reading database ... 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Processing triggers for libc-bin (2.37-15) ... 2m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-yf', 'dist-upgrade'] 2m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m11.6s DUMP: 927d67e88a5444ad4e9d652aa3f273fe - 2m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'show', '--no-all-versions', 'python3-nanoget'] 2m11.9s DUMP: Package: python3-nanoget Source: python-nanoget Version: 1.19.3-1 Installed-Size: 52 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3-numpy, python3-pandas (>= 2.0.0), python3-pysam, python3:any, python3-nanomath Description-en: extract information from Oxford Nanopore sequencing data and alignments The Python3 module nanoget provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments. . Data can be presented in the following formats, using the following functions: . * sorted bam file process_bam(bamfile, threads) * standard fastq file process_fastq_plain(fastqfile, 'threads') * fastq file with metadata from MinKNOW or Albacore process_fastq_rich(fastqfile) * sequencing_summary file generated by Albacore process_summary(sequencing_summary.txt, 'readtype') . Fastq files can be compressed using gzip, bzip2 or bgzip. The data is returned as a pandas DataFrame with standardized headernames for convenient extraction. The functions perform logging while being called and extracting data. Description-md5: b717656953ba87a065e49966061c1863 Homepage: https://github.com/wdecoster/nanoget Section: python Priority: optional Filename: pool/main/p/python-nanoget/python3-nanoget_1.19.3-1_all.deb Size: 11700 MD5sum: b27c8749ed1dec14ef9ed4d10ff99a5f SHA256: a69909d14fdd8d5ed3137c6a6864ab1562467bf49c44d37b55cfac7d65735510 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'show', '--no-all-versions', 'python3-nanoget'] 2m11.9s INFO: apt-cache knows about the following packages: python3-nanoget 2m11.9s INFO: Running scripts pre_install 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 2m12.0s 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: 2m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 2m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 2m12.0s DUMP: python3-nanoget: Installed: 1.19.3-1 Candidate: 1.19.3-1 Version table: *** 1.19.3-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 2m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget'] 2m12.6s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-nanoget is already the newest version (1.19.3-1). The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget'] 2m12.6s INFO: Running scripts post_install 2m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 2m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 2m12.6s INFO: Running scripts post_distupgrade 2m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_exceptions'] 2m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_exceptions'] 2m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_zz_backports'] 2m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_distupgrade_zz_backports'] 2m12.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m14.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m14.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m15.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m15.4s INFO: Running scripts pre_install 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 2m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_database-server'] 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 2m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_exceptions'] 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 2m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_extras'] 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 2m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture'] 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 2m15.5s 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: 2m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy'] 2m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 2m15.5s DUMP: python3-nanoget: Installed: 1.19.3-1 Candidate: 1.19.3-1 Version table: *** 1.19.3-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-cache', 'policy', 'python3-nanoget'] 2m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget=1.19.3-1'] 2m16.1s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-nanoget is already the newest version (1.19.3-1). The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', '-y', 'install', 'python3-nanoget=1.19.3-1'] 2m16.1s INFO: Running scripts post_install 2m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 2m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_install_exceptions'] 2m16.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m17.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 2m17.6s INFO: /bin converted to /usr/bin by /usr merge 2m17.6s INFO: /lib converted to /usr/lib by /usr merge 2m17.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 2m17.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 2m17.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 2m17.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m17.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m17.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m17.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m17.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m17.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 2m17.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m17.6s INFO: /sbin converted to /usr/sbin by /usr merge 2m19.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', '-ac', '--ignore-obsolete'] 2m22.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', '-ac', '--ignore-obsolete'] 2m22.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m22.1s DUMP: 0.15.6 2m22.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m22.1s INFO: Running adequate version 0.15.6 now. 2m22.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'python3-nanoget'] 2m22.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'python3-nanoget'] 2m22.1s INFO: Running scripts pre_remove 2m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_exceptions'] 2m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/pre_remove_exceptions'] 2m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m25.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.10 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 bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.85 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 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+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-extra fonts-dejavu-extra 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-14 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-3 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libblas3:amd64 libblas3 3.12.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.11.8-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-2+b2 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+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.4-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-3 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 14-20240201-3 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 14-20240201-3 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 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 1.6.0-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2+b2 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 3.12.0-2 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+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.42-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 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-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 14-20240201-3 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+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.3 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl3:amd64 libssl3 3.1.5-1 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-3 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255.3-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 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 libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed python3 python3 3.11.6-1 install ok installed python3-biopython python3-biopython 1.81+dfsg-3 install ok installed python3-cairo python3-cairo 1.25.1-2 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-dateutil python3-dateutil 2.8.2-3 install ok installed python3-deprecated python3-deprecated 1.2.14-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-nanoget python3-nanoget 1.19.3-1 install ok installed python3-nanomath python3-nanomath 1.2.1+ds-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-pandas python3-pandas 2.1.4+dfsg-3 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.1.4+dfsg-3 install ok installed python3-pil:amd64 python3-pil 10.2.0-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b1 install ok installed python3-reportlab python3-reportlab 4.0.9-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-tz python3-tz 2023.4-1 install ok installed python3-wrapt python3-wrapt 1.15.0-2+b1 install ok installed python3.11 python3.11 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-minimal python3.12-minimal 3.12.1-2 install ok installed readline-common readline-common 8.2-3 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed util-linux-extra util-linux-extra 2.39.3-6 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 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 2m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3: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', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-dateutil', 'python3-deprecated', 'python3-freetype', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-nanoget'] 3m10.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libdeflate0 libexpat1 libfontconfig1 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 libperl5.38 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsqlite3-0 libssh2-1 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxrender1 mailcap media-types mime-support netbase perl perl-modules-5.36 perl-modules-5.38 python3 python3-biopython python3-cairo python3-chardet python3-dateutil python3-deprecated python3-freetype python3-minimal python3-nanoget python3-nanomath python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pysam python3-reportlab python3-rlpycairo python3-six python3-tz python3-wrapt python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 114 to remove and 0 not upgraded. After this operation, 383 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 ... 16980 files and directories currently installed.) Removing python3-nanoget (1.19.3-1) ... Removing python3-biopython (1.81+dfsg-3) ... Removing python3-reportlab (4.0.9-1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.25.1-2) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing libfontconfig1:amd64 (2.14.2-6+b1) ... Removing fontconfig-config (2.14.2-6+b1) ... 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 python3-nanomath (1.2.1+ds-1) ... Removing python3-pandas (2.1.4+dfsg-3) ... Removing python3-pandas-lib:amd64 (2.1.4+dfsg-3) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblapack3:amd64 (3.12.0-2) ... Removing libblas3:amd64 (3.12.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-pil:amd64 (10.2.0-1) ... Removing libraqm0:amd64 (0.10.1-1) ... Removing python3-pysam (0.22.0+ds-1+b1) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing python3-deprecated (1.2.14-1) ... Removing python3-wrapt (1.15.0-2+b1) ... Removing python3-dateutil (2.8.2-3) ... Removing python3-six (1.16.0-4) ... Removing libfontenc1:amd64 (1:1.1.4-1+b2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl (5.38.2-3) ... Removing libperl5.38:amd64 (5.38.2-3) ... Removing libgdbm-compat4:amd64 (1.23-5) ... Removing libgdbm6:amd64 (1.23-5) ... Removing libgfortran5:amd64 (14-20240201-3) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libglib2.0-0:amd64 (2.78.3-2) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgomp1:amd64 (14-20240201-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libhtscodecs2:amd64 (1.6.0-1) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b2) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing libquadmath0:amd64 (14-20240201-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... 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 (1.11.0-4) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing perl-modules-5.38 (5.38.2-3) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-freetype (2.4.0-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-tz (2023.4-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... 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 (0.11.8-1) ... Removing python3 (3.11.6-1) ... Removing python3-minimal (3.11.6-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing python3.11 (3.11.7-2) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3) ... 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+b2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing libtirpc-common (1.3.4+ds-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Removing python3.11-minimal (3.11.7-2) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Processing triggers for libc-bin (2.37-15) ... 3m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'remove', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3: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', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-dateutil', 'python3-deprecated', 'python3-freetype', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-nanoget'] 3m10.9s INFO: Running scripts post_remove 3m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_remove_exceptions'] 3m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_remove_exceptions'] 3m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3: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', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-dateutil', 'python3-deprecated', 'python3-freetype', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m11.4s DUMP: (Reading database ... 5398 files and directories currently installed.) Purging configuration files for fontconfig-config (2.14.2-6+b1) ... 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 libblas3 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 libcairo2 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 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 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 (2.78.3-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... 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 libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl2 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 libperl5.38 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 libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib 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 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 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 libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed Purging configuration files for 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 (5.38.2-3) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-deprecated which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-nanomath which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3.11 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 Purging configuration files for python3.12-minimal (3.12.1-2) ... Purging configuration files for readline-common (8.2-3) ... 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 (0.19) ... 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3: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', 'mailcap', 'media-types', 'mime-support', 'netbase', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'python3', 'python3-biopython', 'python3-cairo', 'python3-chardet', 'python3-dateutil', 'python3-deprecated', 'python3-freetype', 'python3-minimal', 'python3-nanomath', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pysam', 'python3-reportlab', 'python3-rlpycairo', 'python3-six', 'python3-tz', 'python3-wrapt', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', 'python3-nanoget'] 3m11.4s DUMP: dpkg: warning: ignoring request to remove python3-nanoget which isn't installed 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', 'python3-nanoget'] 3m11.4s INFO: Running scripts post_purge 3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_purge_exceptions'] 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_purge_exceptions'] 3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', '--pending'] 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--purge', '--pending'] 3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--remove', '--pending'] 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg', '--remove', '--pending'] 3m11.4s INFO: Running scripts post_test 3m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_test_exceptions'] 3m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'tmp/scripts/post_test_exceptions'] 3m11.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 3m11.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 3m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-divert', '--list'] 3m11.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 3m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'dpkg-divert', '--list'] 3m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'clean'] 3m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy', 'apt-get', 'clean'] 3m11.9s DEBUG: Recording chroot state 3m13.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/shm'] 3m13.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/shm'] 3m13.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/console'] 3m13.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/console'] 3m13.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/ptmx'] 3m13.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/ptmx'] 3m13.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts'] 3m13.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/dev/pts'] 3m13.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/proc'] 3m13.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy/proc'] 3m13.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 3m13.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmcu_70iy'] 3m13.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmcu_70iy 3m13.3s INFO: PASS: Upgrading between Debian distributions. 3m13.3s INFO: PASS: All tests. 3m13.3s INFO: piuparts run ends. ret=0 End: 2024-02-04 15:47:23 GMT