Start: 2024-02-01 23:50:48 GMT [stable] Package: ariba Source: ariba (2.14.6+ds-1) Version: 2.14.6+ds-1+b2 Installed-Size: 20456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.10), python3 (>= 3.9~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.14), libfml0 (>= 0.1-4~), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Suggests: spades Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.6+ds-1+b2_amd64.deb Size: 1956508 MD5sum: 812917666551065237b70cea18a30bf8 SHA256: bdf34c9be56b76db56966a4c60d2577001324d15cde4d538ba7d4d2a343dee7d [testing] Package: ariba Source: ariba (2.14.6+ds-5) Version: 2.14.6+ds-5+b1 Installed-Size: 20451 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.12), python3 (>= 3.11~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-tk Suggests: spades Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.6+ds-5+b1_amd64.deb Size: 1955700 MD5sum: 88294a49bef761bf606351ec157c8106 SHA256: 8088fc561585993547cc7b1c332ed34e72e75390d566486c1b9fc7e378a4beb6 [sid] Package: ariba Version: 2.14.7+ds-2 Installed-Size: 20588 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.13), python3 (>= 3.11~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-tk Suggests: spades Description: Antibiotic Resistance Identification By Assembly Homepage: https://github.com/sanger-pathogens/ariba Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-2_amd64.deb Size: 1955400 MD5sum: 09380fd97570a468b678a9818f4a1875 SHA256: 51fc8d3cc7191406d288601dc9b3d308462975917b8378862135f4415d38893b 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/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt ariba=2.14.7+ds-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311836~1.3-2-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/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt ariba=2.14.7+ds-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmp3iixfe45 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp3iixfe45 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp3iixfe45/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 0m3.3s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', '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/tmp3iixfe45', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.1s INFO: Running scripts post_setup 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_dummy_users'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s 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' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u2 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1+deb11u10 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m5.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 0m5.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 0m5.9s INFO: Running scripts is_testable 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s INFO: Running scripts pre_test 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_test_root_password'] 0m5.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_test_root_password'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m6.2s DUMP: Package: ariba Source: ariba (2.14.6+ds-1) Version: 2.14.6+ds-1+b2 Installed-Size: 20456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 3.12.0), python3 (<< 3.10), python3 (>= 3.9~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.14), libfml0 (>= 0.1-4~), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Suggests: spades Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.6+ds-1+b2_amd64.deb Size: 1956508 MD5sum: 812917666551065237b70cea18a30bf8 SHA256: bdf34c9be56b76db56966a4c60d2577001324d15cde4d538ba7d4d2a343dee7d 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 0m6.2s INFO: apt-cache knows about the following packages: ariba 0m6.2s INFO: Running scripts pre_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 0m6.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 0m6.3s DUMP: ariba: Installed: (none) Candidate: 2.14.6+ds-1+b2 Version table: 2.14.6+ds-1+b2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 0m32.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blt bowtie2 cd-hit fastaq fontconfig-config fonts-lyx gawk libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libcurl3-gnutls libdeflate0 libexpat1 libfml0 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libgsl25 libgslcblas0 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 libldap-2.4-2 libmd0 libminimap0 libmpdec3 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libtbb2 libtcl8.6 libtiff5 libtk8.6 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 mailcap mash media-types mime-support mummer perl perl-modules-5.32 python-matplotlib-data python3 python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-six python3-soupsieve python3-tk python3.9 python3.9-minimal readline-common samtools sensible-utils tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common Suggested packages: spades blt-demo bowtie2-examples gawk-doc gdbm-l10n gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-renderpm python3-psycopg2 python3-scipy raxml t-coffee wise w3-dtd-mathml python-cycler-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pil-doc python3-pil-dbg python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc tix python3-tk-dbg python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool Recommended packages: ca-certificates javascript-common libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-chardet python3-lxml python3-olefile python3-renderpm The following NEW packages will be installed: ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-lyx gawk libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libcurl3-gnutls libdeflate0 libexpat1 libfml0 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libgsl25 libgslcblas0 libhts3 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 libldap-2.4-2 libmd0 libminimap0 libmpdec3 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libtbb2 libtcl8.6 libtiff5 libtk8.6 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 mailcap mash media-types mime-support mummer perl perl-modules-5.32 python-matplotlib-data python3 python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-six python3-soupsieve python3-tk python3.9 python3.9-minimal readline-common samtools sensible-utils tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common 0 upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 52.9 MB of archives. After this operation, 217 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u2 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u2 [4106 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u2 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libmpfr6 amd64 4.1.0-3 [2012 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 gawk amd64 1:5.1.0-1 [605 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u9 [344 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 fastaq all 3.17.0-3 [47.8 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:43 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python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 python3-soupsieve all 2.2.1-1 [34.7 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 python3-bs4 all 4.9.3-1 [112 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 python3-dendropy all 4.5.1-1 [273 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get:78 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 python3-pymummer all 0.11.0-2 [11.3 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libminimap0 amd64 0.2-5 [22.9 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 cd-hit amd64 4.8.1-3 [522 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libcapnp-0.7.0 amd64 0.7.0-7 [1048 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libmurmurhash2 amd64 1.5-2 [5780 B] Get:93 http://deb.debian.org/debian bullseye/main amd64 mash amd64 2.2.2+dfsg-2 [153 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [772 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 python3-tk amd64 3.9.2-1 [101 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 ariba amd64 2.14.6+ds-1+b2 [1957 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.9 MB in 2s (25.0 MB/s) Selecting previously unselected package perl-modules-5.32. 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Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libcapnp-0.7.0:amd64 (0.7.0-7) ... Setting up libfml0:amd64 (0.1+git20190320.b499514-1+b1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libminimap0 (0.2-5) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... 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 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up mash (2.2.2+dfsg-2) ... Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up libwebpmux3:amd64 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... 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 (1.14-3) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1+deb11u2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u2) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up python3 (3.9.2-3) ... Setting up samtools (1.11-1) ... Setting up python3-six (1.16.0-2) ... Setting up perl (5.32.1-4+deb11u2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.59-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up mummer (3.23+dfsg-7) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up mailcap (3.69) ... Setting up python3-soupsieve (2.2.1-1) ... Setting up cd-hit (4.8.1-3) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up mime-support (3.66) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up fastaq (3.17.0-3) ... Setting up python3-bs4 (4.9.3-1) ... Setting up python3-pymummer (0.11.0-2) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-reportlab (3.5.59-2) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-dendropy (4.5.1-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-tk:amd64 (3.9.2-1) ... Setting up ariba (2.14.6+ds-1+b2) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 0m32.4s INFO: Running scripts post_install 0m32.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 0m32.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 0m32.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 0m33.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 0m33.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3iixfe45 to testing 0m33.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m33.1s INFO: Running scripts pre_distupgrade 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_exceptions'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 0m36.8s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8787 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 3s (5572 kB/s) Reading package lists... 0m36.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 0m36.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-yf', 'dist-upgrade'] 2m58.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libcapnp-0.7.0 libldap-2.4-2 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal ucf Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libgsl25 libsemanage1 The following NEW packages will be installed: binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-12 fonts-dejavu-core fonts-urw-base35 g++ g++-12 gcc gcc-12 gcc-12-base libasan8 libatomic1 libbinutils libboost-dev libboost1.74-dev libc-dev-bin libc6-dev libcap2 libcapnp-0.9.2 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libexpat1-dev libffi8 libfile-find-rule-perl libfontenc1 libfribidi0 libgcc-12-dev libglib2.0-0 libgprofng0 libgraphite2-3 libgsl27 libharfbuzz0b libhtscodecs2 libicu72 libisl23 libitm1 libjansson4 libjs-sphinxdoc libjs-underscore liblbfgsb0 libldap-2.5-0 liblerc4 liblsan0 libmpc3 libnsl-dev libnumber-compare-perl libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.36 libpython3-all-dev libpython3-dev libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 libsemanage2 libsepol2 libssl3 libstdc++-12-dev libtext-glob-perl libtiff6 libtirpc-dev libtsan2 libubsan1 libwebp7 libxml2 libxsimd-dev libxslt1.1 linux-libc-dev perl-modules-5.36 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-contourpy python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-lib2to3 python3-lxml python3-lz4 python3-mpmath python3-packaging python3-pil.imagetk python3-ply python3-pythran python3-renderpm python3-scipy python3-sympy python3-tz python3-ufolib2 python3.11 python3.11-dev python3.11-minimal rpcsvc-proto sgml-base unicode-data usrmerge util-linux-extra w3c-sgml-lib xfonts-encodings xfonts-utils xml-core zlib1g-dev The following packages will be upgraded: adduser apt ariba base-files base-passwd bash bowtie2 bsdutils cd-hit coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs fastaq findutils fontconfig-config fonts-lyx gawk gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg6.0 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libcurl3-gnutls libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libfontconfig1 libfreetype6 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgslcblas0 libgssapi-krb5-2 libhogweed6 libhts3 libidn2-0 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblz4-1 liblzma5 libmd0 libminimap0 libmount1 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libpsl5 libpython3-stdlib libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsigsegv2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libtinfo6 libtirpc-common libtirpc3 libtk8.6 libudev1 libunistring2 libuuid1 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxcb1 libxext6 libxft2 libxrender1 libxxhash0 libzstd1 login logsave lsb-base mailcap mash mawk media-types mount mummer ncurses-base ncurses-bin passwd perl perl-base python-matplotlib-data python3 python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-kiwisolver python3-matplotlib python3-minimal python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-six python3-soupsieve python3-tk readline-common samtools sed sensible-utils sysvinit-utils tar ttf-bitstream-vera tzdata ucf util-linux x11-common zlib1g 176 upgraded, 118 newly installed, 2 to remove and 0 not upgraded. Need to get 242 MB of archives. After this operation, 878 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u4 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u3 [2755 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u3 [606 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+b1 [147 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+b1 [166 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+b1 [107 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+b1 [111 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+b1 [1177 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2 [836 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B] Get:23 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b2 [1491 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+b1 [94.4 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.19-1~deb12u1 [331 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.19-1~deb12u1 [108 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u1 [1404 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+b3 [46.6 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B] Get:81 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:83 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:84 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 35 [12.5 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libcapnp-0.9.2 amd64 0.9.2-2 [1305 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 mash amd64 2.3+dfsg-3+b1 [188 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-5 [108 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-5 [941 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libmurmurhash2 amd64 1.5-3 [5860 B] Get:94 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+b1 [134 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 gawk amd64 1:5.2.1-2 [673 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 ariba amd64 2.14.6+ds-5+b1 [1956 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 ttf-bitstream-vera all 1.10-8.2 [223 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:126 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:140 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+b1 [28.8 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get:190 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1 [690 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B] Get:197 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:208 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB] Get:214 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B] Get:215 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u3 [45.2 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.66-1 [1905 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u3 [1898 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB] Get:224 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B] Get:225 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:230 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get:235 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get:236 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get:239 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get:244 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:246 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:247 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get:251 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 fastaq all 3.17.0-5 [48.2 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 python3-soupsieve all 2.3.2-1 [38.8 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 python3-bs4 all 4.11.2-2 [121 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 python3-dendropy all 4.5.2-1 [275 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 python3-pymummer all 0.11.0-3 [11.4 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 libminimap0 amd64 0.2-7 [21.8 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 cd-hit amd64 4.8.1-4 [522 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:282 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:289 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:291 http://deb.debian.org/debian bookworm/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 242 MB in 3s (85.6 MB/s) (Reading database ... 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Preparing to unpack .../util-linux-extra_2.38.1-5+b1_amd64.deb ... Unpacking util-linux-extra (2.38.1-5+b1) ... Setting up util-linux-extra (2.38.1-5+b1) ... (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 ... 14866 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.4.1-0.2) over (5.2.5-2.1~deb11u1) ... Setting up liblzma5:amd64 (5.4.1-0.2) ... (Reading database ... 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Setting up libtinfo6:amd64 (6.4-4) ... (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 ... 14875 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4-4_amd64.deb ... Unpacking ncurses-bin (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4-4) ... (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 ... 16803 files and directories currently installed.) Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.77) ... Setting up debconf (1.5.82) ... (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 ... 16802 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.33-2) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... (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 ... 16802 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) over (1.19-2) ... Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-2+deb11u2) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-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 ... 16802 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_amd64.deb ... Unpacking sed (4.9-1) over (4.7-1) ... Setting up sed (4.9-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16805 files and directories currently installed.) Preparing to unpack .../libstdc++6_12.2.0-14_amd64.deb ... Unpacking libstdc++6:amd64 (12.2.0-14) over (10.2.1-6) ... Setting up libstdc++6:amd64 (12.2.0-14) ... (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 ... 16805 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-1_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1) over (1.9.3-2) ... Setting up liblz4-1:amd64 (1.9.4-1) ... Selecting previously unselected package libcap2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16805 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-4_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-4) ... (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 ... 16813 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.19-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.19-1~deb12u1) over (247.3-7+deb11u4) ... Setting up libsystemd0:amd64 (252.19-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16814 files and directories currently installed.) Preparing to unpack .../libudev1_252.19-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.19-1~deb12u1) over (247.3-7+deb11u4) ... Setting up libudev1:amd64 (252.19-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16815 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.1-1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.1-1) over (0.8.0-2) ... Setting up libxxhash0:amd64 (0.8.1-1) ... (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 ... 16815 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.6.1_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.6.1) over (2.2.4) ... Setting up libapt-pkg6.0:amd64 (2.6.1) ... (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 ... 16815 files and directories currently installed.) Preparing to unpack .../libnettle8_3.8.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libnettle8:amd64 (3.8.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16815 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.8.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libhogweed6:amd64 (3.8.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16815 files and directories currently installed.) Preparing to unpack .../libunistring2_1.0-2_amd64.deb ... Unpacking libunistring2:amd64 (1.0-2) over (0.9.10-4) ... Setting up libunistring2:amd64 (1.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16815 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.3-1+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.3-1+b1) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.3-1+b1) ... Selecting previously unselected package libffi8:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16817 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-1) ... (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 ... 16822 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.1-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.24.1-2) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.24.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16822 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16822 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u1_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u1) over (3.7.1-5+deb11u3) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16824 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1_all.deb ... Unpacking libsemanage-common (3.4-1) over (3.1-1) ... Setting up libsemanage-common (3.4-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16824 files and directories currently installed.) Preparing to unpack .../libsepol2_3.4-2.1_amd64.deb ... Unpacking libsepol2:amd64 (3.4-2.1) ... Setting up libsepol2:amd64 (3.4-2.1) ... Selecting previously unselected package libsemanage2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16828 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1+b5_amd64.deb ... Unpacking libsemanage2:amd64 (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.4-1+b5) ... (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 ... 16863 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Replacing files in old package libpam-modules:amd64 (1.4.0-9+deb11u1) ... Setting up libpam-modules-bin (1.5.2-6+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16870 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam-modules:amd64 (1.5.2-6+deb12u1) ... Installing new version of config file /etc/security/limits.conf ... Installing new version of config file /etc/security/sepermit.conf ... (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 ... 16871 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.134_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.134) over (3.118+deb11u1) ... Setting up adduser (3.134) ... Installing new version of config file /etc/deluser.conf ... (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 ... 16839 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-1.1_amd64.deb ... Unpacking gpgv (2.2.40-1.1) over (2.2.27-2+deb11u2) ... Setting up gpgv (2.2.40-1.1) ... (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 ... 16839 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.3+deb12u1_all.deb ... Unpacking debian-archive-keyring (2023.3+deb12u1) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.3+deb12u1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (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 ... 16839 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1+b3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-1+b3) over (2.5.1-1+deb11u1) ... Setting up libseccomp2:amd64 (2.5.4-1+b3) ... (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 ... 16840 files and directories currently installed.) Preparing to unpack .../archives/apt_2.6.1_amd64.deb ... Unpacking apt (2.6.1) over (2.2.4) ... Setting up apt (2.6.1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... (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 ... 16837 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.270_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.270) over (0.260) ... Setting up libdebconfclient0:amd64 (0.270) ... (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 ... 16837 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.1_amd64.deb ... Unpacking base-passwd (3.6.1) over (3.5.51) ... Setting up base-passwd (3.6.1) ... Selecting previously unselected package libnumber-compare-perl. (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 ... 16837 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (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 ... 16844 files and directories currently installed.) Preparing to unpack .../libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Setting up libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. (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 ... 16851 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 16866 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_35_all.deb ... Unpacking usrmerge (35) ... Setting up usrmerge (35) ... (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 ... 16873 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.65.2_all.deb ... Unpacking init-system-helpers (1.65.2) over (1.60) ... Setting up init-system-helpers (1.65.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16873 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4-4_all.deb ... Unpacking ncurses-base (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4-4) ... Selecting previously unselected package libssl3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16875 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libcapnp-0.9.2:amd64. Preparing to unpack .../libcapnp-0.9.2_0.9.2-2_amd64.deb ... Unpacking libcapnp-0.9.2:amd64 (0.9.2-2) ... Preparing to unpack .../mash_2.3+dfsg-3+b1_amd64.deb ... Unpacking mash (2.3+dfsg-3+b1) over (2.2.2+dfsg-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16905 files and directories currently installed.) Removing libgsl25:amd64 (2.6+dfsg-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16892 files and directories currently installed.) Preparing to unpack .../libgslcblas0_2.7.1+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.7.1+dfsg-5) over (2.6+dfsg-2) ... Selecting previously unselected package libgsl27:amd64. Preparing to unpack .../libgsl27_2.7.1+dfsg-5_amd64.deb ... Unpacking libgsl27:amd64 (2.7.1+dfsg-5) ... Preparing to unpack .../libmurmurhash2_1.5-3_amd64.deb ... Unpacking libmurmurhash2:amd64 (1.5-3) over (1.5-2) ... Preparing to unpack .../logsave_1.47.0-2_amd64.deb ... Unpacking logsave (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.47.0-2_amd64.deb ... Unpacking libext2fs2:amd64 (1.47.0-2) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.47.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16904 files and directories currently installed.) Preparing to unpack .../00-e2fsprogs_1.47.0-2_amd64.deb ... Unpacking e2fsprogs (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../01-mount_2.38.1-5+b1_amd64.deb ... Unpacking mount (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Preparing to unpack .../02-gawk_1%3a5.2.1-2_amd64.deb ... Unpacking gawk (1:5.2.1-2) over (1:5.1.0-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../03-libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Preparing to unpack .../04-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) over (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../05-python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Preparing to unpack .../06-python3-tk_3.11.2-3_amd64.deb ... 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Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up logsave (1.47.0-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libcapnp-0.9.2:amd64 (0.9.2-2) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up mount (2.38.1-5+b1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up mawk (1.3.4.20200120-3.1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.40-2) ... Setting up libisl23:amd64 (0.25-1) ... Setting up libc-dev-bin (2.36-9+deb12u3) ... Setting up python-matplotlib-data (3.6.3-1) ... Installing new version of config file /etc/matplotlibrc ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libcc1-0:amd64 (12.2.0-14) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libctf0:amd64 (2.40-2) ... Setting up cd-hit (4.8.1-4) ... Setting up liblapack3:amd64 (3.11.0-2) ... Setting up cpp-12 (12.2.0-14) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up e2fsprogs (1.47.0-2) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libgprofng0:amd64 (2.40-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up mash (2.3+dfsg-3+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up cpp (4:12.2.0-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up binutils-x86-64-linux-gnu (2.40-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up gawk (1:5.2.1-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u4) ... Setting up binutils (2.40-2) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up gcc-12 (12.2.0-14) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up mummer (3.23+dfsg-8) ... Setting up libc6-dev:amd64 (2.36-9+deb12u3) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-tz (2022.7.1-4) ... Setting up gcc (4:12.2.0-3) ... Setting up samtools (1.16.1-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.3.2-1) ... Setting up g++-12 (12.2.0-14) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-ply (3.11-5) ... Setting up fastaq (3.17.0-5) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up python3-bs4 (4.11.2-2) ... Setting up python3-pymummer (0.11.0-3) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up g++ (4:12.2.0-3) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up python3-dendropy (4.5.2-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for debianutils (5.7-0.5~deb12u1) ... 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 ariba (2.14.6+ds-5+b1) ... 2m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-yf', 'dist-upgrade'] 2m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m59.6s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 2m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 2m60.0s DUMP: Package: ariba Source: ariba (2.14.6+ds-5) Version: 2.14.6+ds-5+b1 Installed-Size: 20451 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.12), python3 (>= 3.11~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-tk Suggests: spades Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.6+ds-5+b1_amd64.deb Size: 1955700 MD5sum: 88294a49bef761bf606351ec157c8106 SHA256: 8088fc561585993547cc7b1c332ed34e72e75390d566486c1b9fc7e378a4beb6 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 2m60.0s INFO: apt-cache knows about the following packages: ariba 2m60.0s INFO: Running scripts pre_install 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 3m0.0s 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: 3m0.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 3m0.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 3m0.1s DUMP: ariba: Installed: 2.14.6+ds-5+b1 Candidate: 2.14.6+ds-5+b1 Version table: *** 2.14.6+ds-5+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 3m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 3m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 3m0.7s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.14.6+ds-5+b1). The following packages were automatically installed and are no longer required: libcapnp-0.7.0 libldap-2.4-2 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 perl-modules-5.32 python3.9 python3.9-minimal ucf Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 3m0.7s INFO: Running scripts post_install 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 3m0.7s INFO: Running scripts post_distupgrade 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_exceptions'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_exceptions'] 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_zz_backports'] 3m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_zz_backports'] 3m0.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 3m2.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 3m2.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp3iixfe45 to sid 3m2.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 3m2.6s INFO: Running scripts pre_distupgrade 3m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 3m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 3m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_exceptions'] 3m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_exceptions'] 3m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 3m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 3m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_database-server'] 3m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_database-server'] 3m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 3m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 3m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 3m7.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9711 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7130 kB] Fetched 17.0 MB in 3s (4904 kB/s) Reading package lists... 3m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'update'] 3m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-yf', 'dist-upgrade'] 5m9.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libcapnp-0.7.0 libcapnp-0.9.2 libldap-2.4-2 libmpdec3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.32 libperl5.36 libpython3-all-dev libpython3.12 libpython3.12-dev libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libxsimd-dev perl-modules-5.32 perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev python3.9 python3.9-minimal ttf-bitstream-vera ucf xtl-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libboost1.74-dev python3-renderpm python3-reportlab-accel The following NEW packages will be installed: cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu fonts-dejavu-extra fonts-dejavu-mono g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libboost1.83-dev libcairo2 libcapnp-1.0.1 libgcc-13-dev libhwasan0 libperl5.38 libpixman-1-0 libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libsframe1 libsharpyuv0 libstdc++-13-dev libunistring5 libxcb-render0 libxcb-shm0 netbase perl-modules-5.38 python3-cairo python3-chardet python3-freetype python3-rlpycairo python3-setuptools python3.12 python3.12-dev python3.12-minimal xtl-dev The following packages will be upgraded: adduser apt ariba base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu blt bowtie2 bsdutils coreutils cpp cpp-12 dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs fastaq findutils fontconfig-config fonts-dejavu-core fonts-lyx g++ g++-12 gcc gcc-10-base gcc-12 gcc-12-base gcc-9-base gpgv grep hostname init-system-helpers libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblas3 libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libcurl3-gnutls libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libexpat1-dev libext2fs2 libffi8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgprofng0 libgraphite2-3 libgsl27 libgslcblas0 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libhtscodecs2 libicu72 libidn2-0 libimagequant0 libisl23 libitm1 libjansson4 libjpeg62-turbo libjs-sphinxdoc libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblz4-1 liblzma5 libmd0 libminimap0 libmount1 libmpc3 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl3 libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxml2 libxsimd-dev libxxhash0 libzstd1 linux-libc-dev login logsave mash mawk media-types mount ncurses-base ncurses-bin passwd perl perl-base python3 python3-all python3-all-dev python3-appdirs python3-attr python3-biopython python3-brotli python3-bs4 python3-contourpy python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-fonttools python3-fs python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-pymummer python3-pyparsing python3-pysam python3-pythran python3-reportlab python3-scipy python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 python3.11 python3.11-dev python3.11-minimal readline-common samtools sed sensible-utils sysvinit-utils tar tk8.6-blt2.5 tzdata unicode-data usrmerge util-linux util-linux-extra xml-core zlib1g zlib1g-dev 253 upgraded, 41 newly installed, 3 to remove and 0 not upgraded. Need to get 303 MB of archives. After this operation, 459 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 libnsl-dev amd64 1.3.0-3 [66.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15 [1906 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15 [46.9 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1 [188 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2+b2 [9140 B] Get:17 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.4-2 [2058 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:21 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.6.13-1 [2229 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15 [2750 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:24 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240201-1 [42.3 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240201-1 [71.6 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:27 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240201-1 [714 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:33 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:34 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-4+b2 [27.6 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-2 [362 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-2 [124 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:39 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3+b1 [919 kB] Get:40 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.10 [982 kB] Get:42 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:43 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:44 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:45 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:46 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:47 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:48 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3+b1 [616 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:53 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:54 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:56 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:57 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:61 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6 [159 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6 [190 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2 [11.3 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-1 [16.9 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2 [48.4 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6 [117 kB] Get:70 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-6 [155 kB] Get:71 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-6 [1230 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:81 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:82 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.85 [119 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1+b1 [65.8 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:85 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1+b1 [50.1 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1+b1 [265 kB] Get:89 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3+b1 [973 kB] Get:90 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:91 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:92 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:94 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.10 [1363 kB] Get:95 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:96 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:97 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:98 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-6 [32.1 kB] Get:99 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-13 [42.5 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240201-1 [136 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240201-1 [25.9 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240201-1 [9304 B] Get:103 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240201-1 [2723 kB] Get:104 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240201-1 [1200 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libisl23 amd64 0.26-3+b2 [652 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1 [713 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libmpc3 amd64 1.3.1-1+b2 [52.1 kB] Get:108 http://deb.debian.org/debian sid/main amd64 g++-12 amd64 12.3.0-14 [10.8 MB] Get:109 http://deb.debian.org/debian sid/main amd64 gcc-12 amd64 12.3.0-14 [19.5 MB] Get:110 http://deb.debian.org/debian sid/main amd64 cpp-12 amd64 12.3.0-14 [9858 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240201-1 [1070 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.3.0-14 [2069 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240201-1 [147 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240201-1 [836 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libcc1-0 amd64 14-20240201-1 [42.2 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.3.0-14 [2432 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240201-1 [2453 kB] Get:118 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-14 [41.2 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.42-2 [771 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libctf0 amd64 2.42-2 [87.0 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.42-2 [151 kB] Get:122 http://deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.42-2 [2209 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libbinutils amd64 2.42-2 [520 kB] Get:124 http://deb.debian.org/debian sid/main amd64 binutils amd64 2.42-2 [80.4 kB] Get:125 http://deb.debian.org/debian sid/main amd64 binutils-common amd64 2.42-2 [2537 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libjansson4 amd64 2.14-2+b2 [39.9 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libsframe1 amd64 2.42-2 [75.5 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240201-1 [1484 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-13 [2538 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-13 [2208 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2 [3552 B] Get:132 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2+b2 [10.6 MB] Get:133 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.81+dfsg-3 [1625 kB] Get:134 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.0.9-1 [674 kB] Get:135 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:136 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:137 http://deb.debian.org/debian sid/main amd64 python3.11-dev amd64 3.11.7-2 [508 kB] Get:138 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libexpat1-dev amd64 2.5.0-2+b2 [150 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libpython3.11-dev amd64 3.11.7-2 [4576 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libpython3.11 amd64 3.11.7-2 [1990 kB] Get:143 http://deb.debian.org/debian sid/main amd64 tzdata all 2023d-1 [257 kB] Get:144 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.0-1 [894 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-6 [29.7 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:149 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:151 http://deb.debian.org/debian sid/main amd64 python3-all-dev amd64 3.11.6-1 [1076 B] Get:152 http://deb.debian.org/debian sid/main amd64 python3-all amd64 3.11.6-1 [1060 B] Get:153 http://deb.debian.org/debian sid/main amd64 libpython3-all-dev amd64 3.11.6-1 [1072 B] Get:154 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.11.6-1 [9460 B] Get:155 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.11.6-1 [26.1 kB] Get:156 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:157 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:158 http://deb.debian.org/debian sid/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:159 http://deb.debian.org/debian sid/main amd64 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-3 [149 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.1-2 [807 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libpython3.12 amd64 3.12.1-2 [2129 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libpython3.12-dev amd64 3.12.1-2 [4942 kB] Get:165 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.1-2 [2185 kB] Get:166 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:167 http://deb.debian.org/debian sid/main amd64 python3.12-dev amd64 3.12.1-2 [506 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:169 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:170 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:173 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:174 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:175 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.11.5-1 [108 kB] Get:176 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.2.0-1 [77.7 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b2 [190 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-2 [1452 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1 [13.7 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:189 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4 [170 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.3 [107 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.3 [308 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.3 [107 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.3 [120 kB] Get:195 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.2.0-1 [525 kB] Get:196 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:197 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:198 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.2-6+b1 [316 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6+b1 [388 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:204 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.25.1-2 [140 kB] Get:205 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:206 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:207 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-extra all 2.37-8 [1792 kB] Get:208 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:210 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:211 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6 [143 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:216 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:217 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.58.0-1 [74.1 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-1 [421 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1 [92.8 kB] Get:226 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19-1 [644 kB] Get:227 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.18+ds-1 [441 kB] Get:228 http://deb.debian.org/debian sid/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.25+ds-2 [4780 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.25+ds-2 [6817 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.25+ds-2 [36.9 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.25+ds-2 [49.6 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-2 [148 kB] Get:234 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-2 [2407 kB] Get:235 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:236 http://deb.debian.org/debian sid/main amd64 python3-soupsieve all 2.5-1 [38.1 kB] Get:237 http://deb.debian.org/debian sid/main amd64 python3-bs4 all 4.12.3-1 [133 kB] Get:238 http://deb.debian.org/debian sid/main amd64 python3-dendropy all 4.6.1-1 [277 kB] Get:239 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.8.2-3 [78.4 kB] Get:240 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.1-1 [145 kB] Get:241 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.0.7-1+b2 [287 kB] Get:242 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:243 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:244 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.10.1-10 [19.7 MB] Get:245 http://deb.debian.org/debian sid/main amd64 python3-attr all 23.2.0-1 [65.5 kB] Get:246 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:247 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.12-7 [3869 kB] Get:248 http://deb.debian.org/debian sid/main amd64 python3-tz all 2023.4-1 [30.8 kB] Get:249 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:250 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-3 [95.3 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:253 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.1.0-1 [2092 kB] Get:254 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:255 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:256 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:257 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.4-1+b2 [80.3 kB] Get:258 http://deb.debian.org/debian sid/main amd64 python3-packaging all 23.2-1 [44.8 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6 [244 kB] Get:260 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.6.3-1+b2 [8166 kB] Get:261 http://deb.debian.org/debian sid/main amd64 python3-pymummer all 0.11.0-4 [18.0 kB] Get:262 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libminimap0 amd64 0.2-8 [22.2 kB] Get:264 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.5.2-1 [1438 kB] Get:265 http://deb.debian.org/debian sid/main amd64 libcapnp-1.0.1 amd64 1.0.1-3+b1 [1460 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libgsl27 amd64 2.7.1+dfsg-6 [936 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6 [107 kB] Get:268 http://deb.debian.org/debian sid/main amd64 mash amd64 2.3+dfsg-6 [194 kB] Get:269 http://deb.debian.org/debian sid/main amd64 ariba amd64 2.14.7+ds-2 [1955 kB] Get:270 http://deb.debian.org/debian sid/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-13 [10.3 MB] Get:271 http://deb.debian.org/debian sid/main amd64 g++ amd64 4:13.2.0-7 [1348 B] Get:272 http://deb.debian.org/debian sid/main amd64 gcc amd64 4:13.2.0-7 [5152 B] Get:273 http://deb.debian.org/debian sid/main amd64 cpp amd64 4:13.2.0-7 [1564 B] Get:274 http://deb.debian.org/debian sid/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7 [4724 B] Get:275 http://deb.debian.org/debian sid/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-13 [19.8 MB] Get:276 http://deb.debian.org/debian sid/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-13 [11.2 MB] Get:277 http://deb.debian.org/debian sid/main amd64 gcc-13 amd64 13.2.0-13 [475 kB] Get:278 http://deb.debian.org/debian sid/main amd64 g++-13 amd64 13.2.0-13 [14.3 kB] Get:279 http://deb.debian.org/debian sid/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7 [1440 B] Get:280 http://deb.debian.org/debian sid/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7 [1200 B] Get:281 http://deb.debian.org/debian sid/main amd64 cpp-13 amd64 13.2.0-13 [1276 B] Get:282 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.0~RC1-2 [187 kB] Get:283 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-2 [36.4 kB] Get:284 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-4 [28.7 kB] Get:285 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.8-1 [125 kB] Get:286 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1+b2 [23.3 kB] Get:287 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:288 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:289 http://deb.debian.org/debian sid/main amd64 xtl-dev all 0.7.5-3 [89.8 kB] Get:290 http://deb.debian.org/debian sid/main amd64 libxsimd-dev amd64 12.1.1-2 [124 kB] Get:291 http://deb.debian.org/debian sid/main amd64 python3-ply all 3.11-6 [63.7 kB] Get:292 http://deb.debian.org/debian sid/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get:293 http://deb.debian.org/debian sid/main amd64 python3-pythran amd64 0.15.0+ds-2 [443 kB] Get:294 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 303 MB in 4s (69.1 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 ... 45671 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) over (6.4-4) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.4-4) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4-4) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (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 ... 45671 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-bin (6.4+20240113-1) ... (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 ... 47607 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... (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 ... 47608 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../libgdbm-compat4_1.23-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../archives/sed_4.9-2_amd64.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (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 ... 47607 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4) ... (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 ... 47607 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2) ... (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 ... 47606 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2_all.deb ... Unpacking libaudit-common (1:3.1.2-2) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47606 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-1) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.4-1) ... (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 ... 47605 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-2) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47605 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-6_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-6) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-6) ... (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 ... 47604 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 ... 47611 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libnettle8:amd64 (3.9.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47611 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-2) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47611 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47611 files and directories currently installed.) Preparing to unpack .../libunistring5_1.1-2_amd64.deb ... Unpacking libunistring5:amd64 (1.1-2) ... Setting up libunistring5:amd64 (1.1-2) ... (Reading database ... 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(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 ... 47617 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 ... (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 ... 47617 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3+b2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3+b2) over (4.19.0-2) ... Setting up libtasn1-6:amd64 (4.19.0-3+b2) ... (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 ... 47618 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 ... 47617 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 ... (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 ... 47617 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (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 ... 47617 files and directories currently installed.) Preparing to unpack .../debconf_1.5.85_all.deb ... Unpacking debconf (1.5.85) over (1.5.82) ... Setting up debconf (1.5.85) ... Installing new version of config file /etc/debconf.conf ... (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 ... 47616 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-9.1+b1_amd64.deb ... Unpacking libpam0g:amd64 (1.5.2-9.1+b1) over (1.5.2-6+deb12u1) ... Setting up libpam0g:amd64 (1.5.2-9.1+b1) ... (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 ... 47616 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (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 ... 47616 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.5-2) ... (Reading database ... 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Setting up python3-matplotlib (3.6.3-1+b2) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for sgml-base (1.31) ... Processing triggers for debianutils (5.16) ... Setting up libfontconfig1:amd64 (2.14.2-6+b1) ... Processing triggers for mailcap (3.70+nmu1) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up python3-cairo (1.25.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-reportlab (4.0.9-1) ... Setting up python3-biopython (1.81+dfsg-3) ... Setting up ariba (2.14.7+ds-2) ... /usr/lib/python3/dist-packages/ariba/external_progs.py:34: SyntaxWarning: invalid escape sequence '\.' 'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')), /usr/lib/python3/dist-packages/ariba/external_progs.py:35: SyntaxWarning: invalid escape sequence '\.' 'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')), /usr/lib/python3/dist-packages/ariba/external_progs.py:36: SyntaxWarning: invalid escape sequence '\.' 'spades': ('--version', re.compile('SPAdes.*v([0-9\.]+)')) Processing triggers for libc-bin (2.37-15) ... 5m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-yf', 'dist-upgrade'] 5m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m10.9s DUMP: 170bc12a17196aae5ff1d0978130f677 - 5m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 5m11.2s DUMP: Package: ariba Version: 2.14.7+ds-2 Installed-Size: 20588 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3 (<< 3.13), python3 (>= 3.11~), python3-biopython, python3-bs4 (>= 4.1.0), python3-dendropy, python3-matplotlib, python3-pymummer, python3-pysam, python3:any, libc6 (>= 2.14), libfml0 (>= 0.1), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), bowtie2, cd-hit, mash, mummer, python3-tk Suggests: spades Description-en: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. Description-md5: 4d8147ab9fb44c5b4617a970175bc18d Homepage: https://github.com/sanger-pathogens/ariba Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::application, use::analysing Section: science Priority: optional Filename: pool/main/a/ariba/ariba_2.14.7+ds-2_amd64.deb Size: 1955400 MD5sum: 09380fd97570a468b678a9818f4a1875 SHA256: 51fc8d3cc7191406d288601dc9b3d308462975917b8378862135f4415d38893b 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'show', '--no-all-versions', 'ariba'] 5m11.2s INFO: apt-cache knows about the following packages: ariba 5m11.2s INFO: Running scripts pre_install 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 5m11.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 5m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 5m11.3s DUMP: ariba: Installed: 2.14.7+ds-2 Candidate: 2.14.7+ds-2 Version table: *** 2.14.7+ds-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 5m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 5m12.0s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.14.7+ds-2). The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libcapnp-0.7.0 libcapnp-0.9.2 libldap-2.4-2 libmpdec3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.32 libperl5.36 libpython3-all-dev libpython3.12 libpython3.12-dev libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libxsimd-dev perl-modules-5.32 perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev python3.9 python3.9-minimal ttf-bitstream-vera ucf xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba'] 5m12.0s INFO: Running scripts post_install 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 5m12.0s INFO: Running scripts post_distupgrade 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_exceptions'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_exceptions'] 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_zz_backports'] 5m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_distupgrade_zz_backports'] 5m12.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m14.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m14.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m16.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m16.9s INFO: Running scripts pre_install 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 5m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_database-server'] 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 5m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_exceptions'] 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 5m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_extras'] 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 5m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture'] 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 5m17.0s 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: 5m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy'] 5m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 5m17.1s DUMP: ariba: Installed: 2.14.7+ds-2 Candidate: 2.14.7+ds-2 Version table: *** 2.14.7+ds-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-cache', 'policy', 'ariba'] 5m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba=2.14.7+ds-2'] 5m17.9s DUMP: Reading package lists... Building dependency tree... Reading state information... ariba is already the newest version (2.14.7+ds-2). The following packages were automatically installed and are no longer required: libboost-dev libboost1.83-dev libcapnp-0.7.0 libcapnp-0.9.2 libldap-2.4-2 libmpdec3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libperl5.32 libperl5.36 libpython3-all-dev libpython3.12 libpython3.12-dev libpython3.9-minimal libpython3.9-stdlib libtbb2 libtiff5 libwebp6 libxsimd-dev perl-modules-5.32 perl-modules-5.36 python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev python3.9 python3.9-minimal ttf-bitstream-vera ucf xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', '-y', 'install', 'ariba=2.14.7+ds-2'] 5m17.9s INFO: Running scripts post_install 5m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 5m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_install_exceptions'] 5m18.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 5m20.6s INFO: /bin converted to /usr/bin by /usr merge 5m20.6s INFO: /lib converted to /usr/lib by /usr merge 5m20.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 5m20.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 5m20.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 5m20.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 5m20.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 5m20.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 5m20.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 5m20.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 5m20.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 5m20.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 5m20.6s INFO: /sbin converted to /usr/sbin by /usr merge 5m23.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', '-ac', '--ignore-obsolete'] 5m30.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', '-ac', '--ignore-obsolete'] 5m30.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m30.4s DUMP: 0.15.6 5m30.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m30.4s INFO: Running adequate version 0.15.6 now. 5m30.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'ariba'] 5m30.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'ariba'] 5m30.5s INFO: Running scripts pre_remove 5m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_exceptions'] 5m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/pre_remove_exceptions'] 5m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m41.0s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.10 install ok installed ariba ariba 2.14.7+ds-2 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed binutils binutils 2.42-2 install ok installed binutils-common:amd64 binutils-common 2.42-2 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.42-2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bowtie2 bowtie2 2.5.2-1 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed cd-hit cd-hit 4.8.1-4 install ok installed coreutils coreutils 9.4-3+b1 install ok installed cpp cpp 4:13.2.0-7 install ok installed cpp-12 cpp-12 12.3.0-14 install ok installed cpp-13 cpp-13 13.2.0-13 install ok installed cpp-13-x86-64-linux-gnu cpp-13-x86-64-linux-gnu 13.2.0-13 install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:13.2.0-7 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 fastaq fastaq 3.17.0-6 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-lyx fonts-lyx 2.4.0~RC1-2 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-7 install ok installed g++ g++ 4:13.2.0-7 install ok installed g++-12 g++-12 12.3.0-14 install ok installed g++-13 g++-13 13.2.0-13 install ok installed g++-13-x86-64-linux-gnu g++-13-x86-64-linux-gnu 13.2.0-13 install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:13.2.0-7 install ok installed gawk gawk 1:5.2.1-2 install ok installed gcc gcc 4:13.2.0-7 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-2 install ok installed gcc-12 gcc-12 12.3.0-14 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-14 install ok installed gcc-13 gcc-13 13.2.0-13 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-13 install ok installed gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu 13.2.0-13 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-4 install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:13.2.0-7 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 libasan8:amd64 libasan8 14-20240201-1 install ok installed libatomic1:amd64 libatomic1 14-20240201-1 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 libbinutils:amd64 libbinutils 2.42-2 install ok installed libblas3:amd64 libblas3 3.12.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-2+b2 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 libc-dev-bin libc-dev-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libc6-dev:amd64 libc6-dev 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 libcapnp-0.7.0:amd64 libcapnp-0.7.0 0.7.0-7 install ok installed libcapnp-0.9.2:amd64 libcapnp-0.9.2 0.9.2-2 install ok installed libcapnp-1.0.1:amd64 libcapnp-1.0.1 1.0.1-3+b1 install ok installed libcc1-0:amd64 libcc1-0 14-20240201-1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.42-2 install ok installed libctf0:amd64 libctf0 2.42-2 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 libexpat1-dev:amd64 libexpat1-dev 2.5.0-2+b2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfml0:amd64 libfml0 0.1+git20190320.b499514-1+b1 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-12-dev:amd64 libgcc-12-dev 12.3.0-14 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-13 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-1 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 14-20240201-1 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 14-20240201-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgprofng0:amd64 libgprofng0 2.42-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-6 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-6 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 libhwasan0:amd64 libhwasan0 14-20240201-1 install ok installed libicu72:amd64 libicu72 72.1-4 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 libisl23:amd64 libisl23 0.26-3+b2 install ok installed libitm1:amd64 libitm1 14-20240201-1 install ok installed libjansson4:amd64 libjansson4 2.14-2+b2 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 libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-3 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2+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 liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 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 liblsan0:amd64 liblsan0 14-20240201-1 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 libminimap0:amd64 libminimap0 0.2-8 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b2 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1 install ok installed libmurmurhash2:amd64 libmurmurhash2 1.5-3 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 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 1.58.0-1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.25+ds-2 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.25+ds-2 install ok installed libopenblas0:amd64 libopenblas0 0.3.25+ds-2 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.25+ds-2 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 libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u2 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-all-dev:amd64 libpython3-all-dev 3.11.6-1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.6-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11:amd64 libpython3.11 3.11.7-2 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.7-2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.7-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.7-2 install ok installed libpython3.12:amd64 libpython3.12 3.12.1-2 install ok installed libpython3.12-dev:amd64 libpython3.12-dev 3.12.1-2 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.1-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.1-2 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6 install ok installed libquadmath0:amd64 libquadmath0 14-20240201-1 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 libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsframe1:amd64 libsframe1 2.42-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.3 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.0-1 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 libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.3.0-14 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-13 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-1 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 libtbb2:amd64 libtbb2 2020.3-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u4 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 libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 14-20240201-1 install ok installed libubsan1:amd64 libubsan1 14-20240201-1 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 libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 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 libxft2:amd64 libxft2 2.3.6-1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxsimd-dev:amd64 libxsimd-dev 12.1.1-2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.6.13-1 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed lsb-base lsb-base 11.6 install ok installed mailcap mailcap 3.70+nmu1 install ok installed mash mash 2.3+dfsg-6 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 mummer mummer 3.23+dfsg-8 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-5.32 perl-modules-5.32 5.32.1-4+deb11u2 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 python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.6-1 install ok installed python3-all python3-all 3.11.6-1 install ok installed python3-all-dev python3-all-dev 3.11.6-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 23.2.0-1 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-biopython python3-biopython 1.81+dfsg-3 install ok installed python3-brotli python3-brotli 1.1.0-2+b3 install ok installed python3-bs4 python3-bs4 4.12.3-1 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-contourpy python3-contourpy 1.0.7-1+b2 install ok installed python3-cycler python3-cycler 0.11.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dendropy python3-dendropy 4.6.1-1 install ok installed python3-dev python3-dev 3.11.6-1 install ok installed python3-distutils python3-distutils 3.11.5-1 install ok installed python3-fonttools python3-fonttools 4.46.0-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-fs python3-fs 2.4.16-3 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-1+b2 install ok installed python3-lib2to3 python3-lib2to3 3.11.5-1 install ok installed python3-lxml:amd64 python3-lxml 5.1.0-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b3 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b2 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-mpmath python3-mpmath 1.2.1-2 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-packaging python3-packaging 23.2-1 install ok installed python3-pil:amd64 python3-pil 10.2.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.2.0-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-ply python3-ply 3.11-6 install ok installed python3-pymummer python3-pymummer 0.11.0-4 install ok installed python3-pyparsing python3-pyparsing 3.1.1-1 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b1 install ok installed python3-pythran python3-pythran 0.15.0+ds-2 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-scipy python3-scipy 1.10.1-10 install ok installed python3-setuptools python3-setuptools 68.1.2-2 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-soupsieve python3-soupsieve 2.5-1 install ok installed python3-sympy python3-sympy 1.12-7 install ok installed python3-tk:amd64 python3-tk 3.11.5-1 install ok installed python3-tz python3-tz 2023.4-1 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3.11 python3.11 3.11.7-2 install ok installed python3.11-dev python3.11-dev 3.11.7-2 install ok installed python3.11-minimal python3.11-minimal 3.11.7-2 install ok installed python3.12 python3.12 3.12.1-2 install ok installed python3.12-dev python3.12-dev 3.12.1-2 install ok installed python3.12-minimal python3.12-minimal 3.12.1-2 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.2-3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed samtools samtools 1.19-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.20 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 tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8.2 install ok installed tzdata tzdata 2023d-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usrmerge usrmerge 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 xtl-dev xtl-dev 0.7.5-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3+b1 5m41.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m41.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'bowtie2', 'cd-hit', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gawk', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libminimap0:amd64', 'libmpc3:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'mailcap', 'mash', 'media-types', 'mime-support', 'mummer', 'netbase', 'perl-modules-5.32', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'rpcsvc-proto', 'samtools', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'ucf', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'xtl-dev', 'zlib1g-dev:amd64', 'ariba'] 6m39.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gcc-12-base libperl5.36 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ariba binutils binutils-common binutils-x86-64-linux-gnu blt bowtie2 cd-hit cpp cpp-12 cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu fastaq fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-12 g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gawk gcc gcc-12 gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libbinutils libblas3 libboost-dev libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcapnp-0.7.0 libcapnp-0.9.2 libcapnp-1.0.1 libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libcurl3-gnutls libdeflate0 libexpat1 libexpat1-dev libfml0 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-13-dev libgfortran5 libglib2.0-0 libgomp1 libgprofng0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libhwasan0 libicu72 libimagequant0 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-2.5-0 liblerc4 liblsan0 libminimap0 libmpc3 libmpdec3 libmpfr6 libmurmurhash2 libncurses6 libncursesw6 libnghttp2-14 libnsl-dev libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libperl5.32 libpixman-1-0 libpng16-16 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.9-minimal libpython3.9-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsframe1 libsharpyuv0 libsigsegv2 libsqlite3-0 libssh2-1 libstdc++-12-dev libstdc++-13-dev libtbb2 libtcl8.6 libtiff5 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 linux-libc-dev mailcap mash media-types mime-support mummer netbase perl-modules-5.32 python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-biopython python3-brotli python3-bs4 python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-fonttools python3-freetype python3-fs python3-gast python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-pymummer python3-pyparsing python3-pysam python3-pythran python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-six python3-soupsieve python3-sympy python3-tk python3-tz python3-ufolib2 python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal python3.9 python3.9-minimal readline-common rpcsvc-proto samtools sensible-utils sgml-base tk8.6-blt2.5 ttf-bitstream-vera ucf unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core xtl-dev zlib1g-dev 0 upgraded, 0 newly installed, 242 to remove and 0 not upgraded. After this operation, 1446 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 ... 51615 files and directories currently installed.) Removing ariba (2.14.7+ds-2) ... Removing python3-pythran (0.15.0+ds-2) ... Removing g++ (4:13.2.0-7) ... Removing gcc (4:13.2.0-7) ... Removing g++-12 (12.3.0-14) ... Removing gcc-12 (12.3.0-14) ... Removing g++-x86-64-linux-gnu (4:13.2.0-7) ... Removing gcc-x86-64-linux-gnu (4:13.2.0-7) ... Removing g++-13 (13.2.0-13) ... Removing g++-13-x86-64-linux-gnu (13.2.0-13) ... Removing python3-biopython (1.81+dfsg-3) ... Removing python3-reportlab (4.0.9-1) ... Removing python3-matplotlib (3.6.3-1+b2) ... Removing python3-pil.imagetk:amd64 (10.2.0-1) ... Removing python3-pil:amd64 (10.2.0-1) ... Removing python3-tk:amd64 (3.11.5-1) ... Removing blt (2.5.3+dfsg-7) ... Removing bowtie2 (2.5.2-1) ... Removing cd-hit (4.8.1-4) ... Removing cpp (4:13.2.0-7) ... Removing cpp-12 (12.3.0-14) ... Removing cpp-13 (13.2.0-13) ... Removing cpp-x86-64-linux-gnu (4:13.2.0-7) ... Removing python3-pymummer (0.11.0-4) ... Removing fastaq (3.17.0-6) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... 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 python-matplotlib-data (3.6.3-1) ... Removing fonts-dejavu-extra (2.37-8) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing fonts-lyx (2.4.0~RC1-2) ... Removing fonts-urw-base35 (20200910-7) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing libboost-dev:amd64 (1.83.0.2) ... Removing libboost1.83-dev:amd64 (1.83.0-2+b2) ... Removing libstdc++-13-dev:amd64 (13.2.0-13) ... Removing libstdc++-12-dev:amd64 (12.3.0-14) ... Removing libgcc-12-dev:amd64 (12.3.0-14) ... Removing python3-contourpy (1.0.7-1+b2) ... Removing liblapack3:amd64 (3.12.0-2) ... Removing libblas3:amd64 (3.12.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing libraqm0:amd64 (0.10.1-1) ... Removing samtools (1.19-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing python3-all-dev (3.11.6-1) ... Removing python3.12-dev (3.12.1-2) ... Removing libpython3-all-dev:amd64 (3.11.6-1) ... Removing libpython3.12-dev:amd64 (3.12.1-2) ... Removing python3-dev (3.11.6-1) ... Removing libpython3-dev:amd64 (3.11.6-1) ... Removing libcapnp-0.7.0:amd64 (0.7.0-7) ... Removing libcapnp-0.9.2:amd64 (0.9.2-2) ... Removing mash (2.3+dfsg-6) ... Removing libcapnp-1.0.1:amd64 (1.0.1-3+b1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u4) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libfml0:amd64 (0.1+git20190320.b499514-1+b1) ... Removing libfontenc1:amd64 (1:1.1.4-1+b2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libopenblas-dev:amd64 (0.3.25+ds-2) ... Removing libopenblas-pthread-dev:amd64 (0.3.25+ds-2) ... Removing libopenblas0:amd64 (0.3.25+ds-2) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libglib2.0-0:amd64 (2.78.3-2) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libgsl27:amd64 (2.7.1+dfsg-6) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-6) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libjs-sphinxdoc (7.2.6-3) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing liblerc4:amd64 (4.0.0+ds-4) ... Removing libminimap0:amd64 (0.2-8) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libmurmurhash2:amd64 (1.5-3) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3.12:amd64 (3.12.1-2) ... Removing python3-pysam (0.22.0+ds-1+b1) ... Removing python3-setuptools (68.1.2-2) ... Removing libopenjp2-7:amd64 (2.5.0-2+b2) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u2) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing python3.11-dev (3.11.7-2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libqhull-r8.0:amd64 (2020.2-6) ... 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 libsigsegv2:amd64 (2.14-1) ... Removing libtbb2:amd64 (2020.3-1) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxsimd-dev:amd64 (12.1.1-2) ... Removing mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... Removing perl-modules-5.32 (5.32.1-4+deb11u2) ... Removing python3-beniget (0.4.1-3) ... Removing python3-bs4 (4.12.3-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-cycler (0.11.0-1) ... Removing python3-dateutil (2.8.2-3) ... Removing python3-dendropy (4.6.1-1) ... Removing python3-freetype (2.4.0-1) ... Removing python3-gast (0.5.2-2) ... Removing python3-kiwisolver (1.4.4-1+b2) ... Removing python3-packaging (23.2-1) ... Removing python3-ply (3.11-6) ... Removing python3-pyparsing (3.1.1-1) ... Removing python3-soupsieve (2.5-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.20) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing ttf-bitstream-vera (1.10-8.2) ... 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 xtl-dev (0.7.5-3) ... Removing gcc-13 (13.2.0-13) ... Removing binutils (2.42-2) ... Removing gcc-13-x86-64-linux-gnu (13.2.0-13) ... Removing binutils-x86-64-linux-gnu (2.42-2) ... Removing libgprofng0:amd64 (2.42-2) ... Removing libctf0:amd64 (2.42-2) ... Removing libbinutils:amd64 (2.42-2) ... Removing binutils-common:amd64 (2.42-2) ... Removing cpp-13-x86-64-linux-gnu (13.2.0-13) ... Removing libgcc-13-dev:amd64 (13.2.0-13) ... Removing gcc-13-base:amd64 (13.2.0-13) ... Removing libasan8:amd64 (14-20240201-1) ... Removing libatomic1:amd64 (14-20240201-1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-1) ... 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 libpython3.11-dev:amd64 (3.11.7-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3+b1) ... Removing libexpat1-dev:amd64 (2.5.0-2+b2) ... Removing libc6-dev:amd64 (2.37-15) ... Removing libc-dev-bin (2.37-15) ... Removing libcc1-0:amd64 (14-20240201-1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... Removing libctf-nobfd0:amd64 (2.42-2) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libgomp1:amd64 (14-20240201-1) ... Removing libhtscodecs2:amd64 (1.6.0-1) ... Removing libhwasan0:amd64 (14-20240201-1) ... Removing libisl23:amd64 (0.26-3+b2) ... Removing libitm1:amd64 (14-20240201-1) ... Removing libjansson4:amd64 (2.14-2+b2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblsan0:amd64 (14-20240201-1) ... Removing libmpc3:amd64 (1.3.1-1+b2) ... Removing libmpfr6:amd64 (4.2.1-1) ... Removing libnghttp2-14:amd64 (1.58.0-1) ... Removing libnsl-dev:amd64 (1.3.0-3) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3.11:amd64 (3.11.7-2) ... Removing libquadmath0:amd64 (14-20240201-1) ... 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 libsframe1:amd64 (2.42-2) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1) ... Removing libtsan2:amd64 (14-20240201-1) ... Removing libubsan1:amd64 (14-20240201-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing linux-libc-dev (6.6.13-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing python3-fonttools (4.46.0-1) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-scipy (1.10.1-10) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Removing python3-all (3.11.6-1) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing libopenblas0-pthread:amd64 (0.3.25+ds-2) ... Removing libgfortran5:amd64 (14-20240201-1) ... Removing python3-lxml:amd64 (5.1.0-1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing python3-distutils (3.11.5-1) ... Removing python3-attr (23.2.0-1) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing python3-fs (2.4.16-3) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-lib2to3 (3.11.5-1) ... Removing python3-lz4 (4.0.2+dfsg-1+b3) ... Removing python3-sympy (1.12-7) ... Removing python3-mpmath (1.2.1-2) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-six (1.16.0-4) ... Removing python3-tz (2023.4-1) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.11.6-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing python3.11 (3.11.7-2) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.7-2) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.45.0-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Processing triggers for libc-bin (2.37-15) ... 6m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'bowtie2', 'cd-hit', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++-', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gawk', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libminimap0:amd64', 'libmpc3:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'mailcap', 'mash', 'media-types', 'mime-support', 'mummer', 'netbase', 'perl-modules-5.32', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'rpcsvc-proto', 'samtools', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'ucf', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'xtl-dev', 'zlib1g-dev:amd64', 'ariba'] 6m39.8s INFO: Running scripts post_remove 6m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_remove_exceptions'] 6m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_remove_exceptions'] 6m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'bowtie2', 'cd-hit', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gawk', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libminimap0:amd64', 'libmpc3:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'mailcap', 'mash', 'media-types', 'mime-support', 'mummer', 'netbase', 'perl-modules-5.32', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'rpcsvc-proto', 'samtools', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'ucf', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'xtl-dev', 'zlib1g-dev:amd64'] 6m40.6s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed (Reading database ... 9476 files and directories currently installed.) Purging configuration files for binutils-common:amd64 (2.42-2) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove cd-hit which isn't installed Purging configuration files for cpp (4:13.2.0-7) ... dpkg: warning: ignoring request to remove cpp-12 which isn't installed dpkg: warning: ignoring request to remove cpp-13 which isn't installed dpkg: warning: ignoring request to remove cpp-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove cpp-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't 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) ... dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-12 which isn't installed dpkg: warning: ignoring request to remove g++-13 which isn't installed dpkg: warning: ignoring request to remove g++-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove g++-x86-64-linux-gnu which isn't installed Purging configuration files for gawk (1:5.2.1-2) ... dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-12 which isn't installed dpkg: warning: ignoring request to remove gcc-13 which isn't installed dpkg: warning: ignoring request to remove gcc-13-base which isn't installed dpkg: warning: ignoring request to remove gcc-13-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove gcc-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.7.0 which isn't installed dpkg: warning: ignoring request to remove libcapnp-0.9.2 which isn't installed dpkg: warning: ignoring request to remove libcapnp-1.0.1 which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-4) ... dpkg: warning: ignoring request to remove libctf-nobfd0 which isn't installed dpkg: warning: ignoring request to remove libctf0 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libfml0 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-13-dev 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 libgprofng0 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgsl27 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl23 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjansson4 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libminimap0 which isn't installed dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmurmurhash2 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 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-all-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.11 which isn't installed dpkg: warning: ignoring request to remove libpython3.11-dev which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.7-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12 which isn't installed dpkg: warning: ignoring request to remove libpython3.12-dev which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.1-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsframe1 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-dev which isn't installed dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxsimd-dev which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... dpkg: warning: ignoring request to remove mash which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python-matplotlib-data (3.6.3-1) ... Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-all which isn't installed dpkg: warning: ignoring request to remove python3-all-dev which isn't installed dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-beniget which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-bs4 which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dendropy which isn't installed dpkg: warning: ignoring request to remove python3-dev which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-gast which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-ply which isn't installed dpkg: warning: ignoring request to remove python3-pymummer which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-pythran which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-soupsieve which isn't installed Purging configuration files for python3-sympy (1.12-7) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.7-2) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed dpkg: warning: ignoring request to remove python3.12-dev which isn't installed Purging configuration files for python3.12-minimal (3.12.1-2) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sgml-base (1.31) ... dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... 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) ... dpkg: warning: ignoring request to remove xtl-dev which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 6m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'bowtie2', 'cd-hit', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-extra', 'fonts-dejavu-mono', 'fonts-lyx', 'fonts-urw-base35', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gawk', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'libasan8:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcapnp-0.7.0:amd64', 'libcapnp-0.9.2:amd64', 'libcapnp-1.0.1:amd64', 'libcc1-0:amd64', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfml0:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhwasan0:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libminimap0:amd64', 'libmpc3:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libmurmurhash2:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'linux-libc-dev', 'mailcap', 'mash', 'media-types', 'mime-support', 'mummer', 'netbase', 'perl-modules-5.32', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-biopython', 'python3-brotli', 'python3-bs4', 'python3-cairo', 'python3-chardet', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dendropy', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-gast', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-ply', 'python3-pymummer', 'python3-pyparsing', 'python3-pysam', 'python3-pythran', 'python3-reportlab', 'python3-rlpycairo', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-soupsieve', 'python3-sympy', 'python3-tk:amd64', 'python3-tz', 'python3-ufolib2', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'rpcsvc-proto', 'samtools', 'sensible-utils', 'sgml-base', 'tk8.6-blt2.5', 'ttf-bitstream-vera', 'ucf', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'xtl-dev', 'zlib1g-dev:amd64'] 6m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', 'ariba'] 6m40.6s DUMP: dpkg: warning: ignoring request to remove ariba which isn't installed 6m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', 'ariba'] 6m40.6s INFO: Running scripts post_purge 6m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_purge_exceptions'] 6m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_purge_exceptions'] 6m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', '--pending'] 6m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--purge', '--pending'] 6m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--remove', '--pending'] 6m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg', '--remove', '--pending'] 6m40.7s INFO: Running scripts post_test 6m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_test_exceptions'] 6m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'tmp/scripts/post_test_exceptions'] 6m40.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 6m41.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 6m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-divert', '--list'] 6m41.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 6m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'dpkg-divert', '--list'] 6m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'clean'] 6m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp3iixfe45', 'apt-get', 'clean'] 6m41.3s DEBUG: Recording chroot state 6m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/shm'] 6m42.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/shm'] 6m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/console'] 6m42.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/console'] 6m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/ptmx'] 6m42.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/ptmx'] 6m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts'] 6m42.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/dev/pts'] 6m42.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/proc'] 6m42.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp3iixfe45/proc'] 6m42.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 6m42.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp3iixfe45'] 6m42.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp3iixfe45 6m42.9s INFO: PASS: Upgrading between Debian distributions. 6m42.9s INFO: PASS: All tests. 6m42.9s INFO: piuparts run ends. ret=0 End: 2024-02-01 23:57:31 GMT