Start: 2024-10-21 04:32:34 GMT [stable] Package: pinfish Version: 0.1.0+ds-3 Installed-Size: 8557 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), minimap2, racon Description: Collection of tools to annotate genomes using long read transcriptomics data Homepage: https://github.com/nanoporetech/pinfish Description-md5: e070704f0ce179f7e25e747b54785f16 Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-3_amd64.deb Size: 1363672 MD5sum: f8d4a0c4a3de070ea3ef7a90dee3702a SHA256: f636843b9acd337876f858f4db277f1d4cda37256d4143072046d1c63a7839df [testing] Package: pinfish Source: pinfish (0.1.0+ds-4) Version: 0.1.0+ds-4+b2 Installed-Size: 8250 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), minimap2, racon Description: Collection of tools to annotate genomes using long read transcriptomics data Homepage: https://github.com/nanoporetech/pinfish Built-Using: golang-1.23 (= 1.23.1-3), golang-github-biogo-biogo (= 1.0.4-1), golang-github-biogo-hts (= 1.4.5+dfsg1-1), golang-github-google-uuid (= 1.6.0-1) Description-md5: e070704f0ce179f7e25e747b54785f16 Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-4+b2_amd64.deb Size: 1408224 MD5sum: 4b1a59819affff06688681034b64cb0e SHA256: e18942da6b2ebd174a53f20132a401beced8318a2a3d7e49bc8ced951e5609a5 [sid] Package: pinfish Source: pinfish (0.1.0+ds-4) Version: 0.1.0+ds-4+b3 Installed-Size: 8254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), minimap2, racon Description: Collection of tools to annotate genomes using long read transcriptomics data Homepage: https://github.com/nanoporetech/pinfish Built-Using: golang-1.23 (= 1.23.2-1), golang-github-biogo-biogo (= 1.0.4-1), golang-github-biogo-hts (= 1.4.5+dfsg1-1), golang-github-google-uuid (= 1.6.0-1) Description-md5: e070704f0ce179f7e25e747b54785f16 Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-4+b3_amd64.deb Size: 1408756 MD5sum: e3c4df4afb5753a53cd6edaa25b350aa SHA256: 63ec45bd2bc43fae3bd512deab8999df165cacbe24a07d37b7919ab8979975c9 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt pinfish=0.1.0+ds-4+b3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt pinfish=0.1.0+ds-4+b3 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp_00_v2_z 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_00_v2_z 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_00_v2_z/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m0.7s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s DUMP: 14b5c1b94e8a6c425b0bba0e4df4ee12 - 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s INFO: Running scripts post_setup 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_minimize'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_setup_zz_backports'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u7 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.30-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.30-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m1.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m1.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m1.8s INFO: Running scripts is_testable 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s INFO: Running scripts pre_test 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_test_root_password'] 0m1.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_test_root_password'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m1.9s DUMP: Package: pinfish Version: 0.1.0+ds-3 Installed-Size: 8557 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.4), minimap2, racon Description-en: Collection of tools to annotate genomes using long read transcriptomics data The toolchain is composed of the following tools: 1. spliced_bam2gff - a tool for converting sorted BAM files containing spliced alignments into GFF2 format. Each read will be represented as a distinct transcript. This tool comes handy when visualizing spliced reads at particular loci and to provide input to the rest of the toolchain. . 2. cluster_gff - this tool takes a sorted GFF2 file as input and clusters together reads having similar exon/intron structure and creates a rough consensus of the clusters by taking the median of exon boundaries from all transcripts in the cluster. . 3. polish_clusters - this tool takes the cluster definitions generated by cluster_gff and for each cluster creates an error corrected read by mapping all reads on the read with the median length and polishing it using racon. The polished reads can be mapped to the genome using minimap2 or GMAP. . 4. collapse_partials - this tool takes GFFs generated by either cluster_gff or polish_clusters and filters out transcripts which are likely to be based on RNA degradation products from the 5' end. The tool clusters the input transcripts into "loci" by the 3' ends and discards transcripts which have a compatible transcripts in the loci with more exons. Description-md5: e070704f0ce179f7e25e747b54785f16 Homepage: https://github.com/nanoporetech/pinfish Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-3_amd64.deb Size: 1363672 MD5sum: f8d4a0c4a3de070ea3ef7a90dee3702a SHA256: f636843b9acd337876f858f4db277f1d4cda37256d4143072046d1c63a7839df 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m1.9s INFO: apt-cache knows about the following packages: pinfish 0m1.9s INFO: Running scripts pre_install 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m2.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.7,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m2.0s DUMP: pinfish: Installed: (none) Candidate: 0.1.0+ds-3 Version table: 0.1.0+ds-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m4.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libedlib1 libspoa7.0.0 minimap2 racon Recommended packages: python3 rampler The following NEW packages will be installed: libedlib1 libspoa7.0.0 minimap2 pinfish racon 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 4951 kB of archives. After this operation, 12.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libedlib1 amd64 1.2.7-4+b1 [17.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libspoa7.0.0 amd64 4.0.8-1 [68.4 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 minimap2 amd64 2.24+dfsg-3+b1 [386 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 racon amd64 1.5.0-3 [3115 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 pinfish amd64 0.1.0+ds-3 [1364 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4951 kB in 1s (3417 kB/s) Selecting previously unselected package libedlib1: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 ... 6093 files and directories currently installed.) Preparing to unpack .../libedlib1_1.2.7-4+b1_amd64.deb ... Unpacking libedlib1:amd64 (1.2.7-4+b1) ... Selecting previously unselected package libspoa7.0.0:amd64. Preparing to unpack .../libspoa7.0.0_4.0.8-1_amd64.deb ... Unpacking libspoa7.0.0:amd64 (4.0.8-1) ... Selecting previously unselected package minimap2. Preparing to unpack .../minimap2_2.24+dfsg-3+b1_amd64.deb ... Unpacking minimap2 (2.24+dfsg-3+b1) ... Selecting previously unselected package racon. Preparing to unpack .../racon_1.5.0-3_amd64.deb ... Unpacking racon (1.5.0-3) ... Selecting previously unselected package pinfish. Preparing to unpack .../pinfish_0.1.0+ds-3_amd64.deb ... Unpacking pinfish (0.1.0+ds-3) ... Setting up minimap2 (2.24+dfsg-3+b1) ... Setting up libspoa7.0.0:amd64 (4.0.8-1) ... Setting up libedlib1:amd64 (1.2.7-4+b1) ... Setting up racon (1.5.0-3) ... Setting up pinfish (0.1.0+ds-3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m4.0s INFO: Running scripts post_install 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m4.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp_00_v2_z to testing 0m4.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m4.2s INFO: Running scripts pre_distupgrade 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m6.0s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9331 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6234 kB] Fetched 15.7 MB in 1s (11.8 MB/s) Reading package lists... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m12.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libapt-pkg6.0 libdb5.3 libext2fs2 libgnutls30 libhogweed6 libnettle8 The following NEW packages will be installed: gcc-14-base libapt-pkg6.0t64 libbsd0 libdb5.3t64 libext2fs2t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libssl3t64 libunistring5 login.defs openssl-provider-legacy The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcom-err2 libcrypt1 libdebconfclient0 libedlib1 libffi8 libgcc-s1 libgcrypt20 libgmp10 libgpg-error0 libidn2-0 liblz4-1 liblzma5 libmd0 libmount1 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libspoa7.0.0 libss2 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libuuid1 libxxhash0 libzstd1 login logsave mawk minimap2 mount ncurses-base ncurses-bin passwd perl-base pinfish sed sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra zlib1g 85 upgraded, 12 newly installed, 6 to remove and 0 not upgraded. Need to get 37.1 MB of archives. After this operation, 12.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.5 [72.8 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.40-3 [2807 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.40-3 [627 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-6 [46.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-6 [72.8 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.20 [89.5 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.32-1+b2 [1500 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.7-2 [382 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-9 [105 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libzstd1 amd64 1.5.6+dfsg-1 [303 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.3.2-1 [2271 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.3.2-1 [298 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1 [87.9 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-9 [93.2 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.50-4 [81.6 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-6 [843 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-6 [715 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10-1 [303 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10-1 [334 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-2 [424 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.6-2 [1444 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.9.4-3 [59.4 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 liblzma5 amd64 5.6.2-2 [254 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.7-2 [145 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.8 [1045 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.8 [1410 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.11 [1531 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 findutils amd64 4.10.0-3 [700 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 grep amd64 3.11-4 [431 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 hostname amd64 3.25 [11.0 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.16.0-4 [185 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:3.1.2-4 [11.5 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-2 [17.2 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:3.1.2-4+b1 [49.0 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libcrypt1 amd64 1:4.4.36-5 [89.8 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.38.2-5 [1643 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 debconf all 1.5.87 [119 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.7-3 [76.9 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.2-9 [81.4 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5-2 [344 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5-2 [433 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 sed amd64 4.9-2 [329 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-9 [168 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-9 [199 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-9 [139 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-9 [35.6 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-9 [1216 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 util-linux-extra amd64 2.40.2-9 [265 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.272 [10.0 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 base-passwd amd64 3.6.4 [50.9 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-2 [131 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libacl1 amd64 2.3.2-2 [32.4 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libattr1 amd64 1:2.5.2-2 [22.7 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.7-2 [7108 B] Get:74 http://deb.debian.org/debian trixie/main amd64 libsepol2 amd64 3.7-1 [293 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.7-2 [91.3 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.16.0-4 [1232 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.44-1 [218 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-1+b1 [47.3 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 usr-is-merged all 39 [5572 B] Get:82 http://deb.debian.org/debian trixie/main amd64 init-system-helpers all 1.67 [38.7 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5-2 [270 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 sysvinit-utils amd64 3.10-3 [33.0 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 logsave amd64 1.47.1-1 [22.7 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libext2fs2t64 amd64 1.47.1-1 [210 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 e2fsprogs amd64 1.47.1-1 [583 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-9 [154 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 mawk amd64 1.3.4.20240905-1 [138 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 gcc-12-base amd64 12.4.0-2 [42.9 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libedlib1 amd64 1.2.7-6 [17.5 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2 [70.5 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libss2 amd64 1.47.1-1 [27.6 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 minimap2 amd64 2.27+dfsg-1+b1 [389 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 pinfish amd64 0.1.0+ds-4+b2 [1408 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 37.1 MB in 2s (20.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6150 files and directories currently installed.) Preparing to unpack .../base-files_13.5_amd64.deb ... Unpacking base-files (13.5) over (12.4+deb12u7) ... Setting up base-files (13.5) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Updating /etc/profile to current default. (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 ... 6163 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14.2.0-6_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-6) ... Setting up gcc-14-base:amd64 (14.2.0-6) ... (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 ... 6168 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-6_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-6) over (12.2.0-14) ... Setting up libgcc-s1:amd64 (14.2.0-6) ... (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 ... 6168 files and directories currently installed.) Preparing to unpack .../debianutils_5.20_amd64.deb ... Unpacking debianutils (5.20) over (5.7-0.5~deb12u1) ... Setting up debianutils (5.20) ... (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 ... 6167 files and directories currently installed.) Preparing to unpack .../bash_5.2.32-1+b2_amd64.deb ... Unpacking bash (5.2.32-1+b2) over (5.2.15-2+b7) ... Setting up bash (5.2.32-1+b2) ... Installing new version of config file /etc/bash.bashrc ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6167 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) over (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-5) ... (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 ... 6167 files and directories currently installed.) Preparing to unpack .../libsystemd0_256.7-2_amd64.deb ... Unpacking libsystemd0:amd64 (256.7-2) over (252.30-1~deb12u2) ... Setting up libsystemd0:amd64 (256.7-2) ... (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 ... 6167 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-9_amd64.deb ... Unpacking bsdutils (1:2.40.2-9) over (1:2.38.1-5+deb12u1) ... Setting up bsdutils (1:2.40.2-9) ... (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 ... 6168 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2+b1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2+b1) over (2:6.2.1+dfsg1-1.1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-2+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 ... 6169 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.6+dfsg-1_amd64.deb ... Unpacking libzstd1:amd64 (1.5.6+dfsg-1) over (1.5.4+dfsg2-5) ... Setting up libzstd1:amd64 (1.5.6+dfsg-1) ... Selecting previously unselected package libssl3t64: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 ... 6169 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.3.2-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.3.2-1) ... Selecting previously unselected package openssl-provider-legacy. Preparing to unpack .../openssl-provider-legacy_3.3.2-1_amd64.deb ... Unpacking openssl-provider-legacy (3.3.2-1) ... Setting up openssl-provider-legacy (3.3.2-1) ... Setting up libssl3t64:amd64 (3.3.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6188 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg+really1.3.1-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg+really1.3.1-1) over (1:1.2.13.dfsg-1) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.1-1) ... (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 ... 6188 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3.1_amd64.deb ... Unpacking coreutils (9.4-3.1) over (9.1-1) ... Setting up coreutils (9.4-3.1) ... (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 ... 6193 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-9_amd64.deb ... Unpacking dash (0.5.12-9) over (0.5.12-2) ... Setting up dash (0.5.12-9) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (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 ... 6190 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_amd64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (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 ... 6192 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.50-4_amd64.deb ... Unpacking libgpg-error0:amd64 (1.50-4) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.50-4) ... (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 ... 6192 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.11.0-6_amd64.deb ... Unpacking libgcrypt20:amd64 (1.11.0-6) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.11.0-6) ... (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 ... 6192 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-6_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-6) over (12.2.0-14) ... Setting up libstdc++6:amd64 (14.2.0-6) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.7~). (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 ... 6192 files and directories currently installed.) Removing libnettle8:amd64 (3.8.1-2) ... Selecting previously unselected package libnettle8t64: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 ... 6184 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10-1) ... Setting up libnettle8t64:amd64 (3.10-1) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 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 ... 6193 files and directories currently installed.) Removing libhogweed6:amd64 (3.8.1-2) ... Selecting previously unselected package libhogweed6t64: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 ... 6187 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10-1) ... Setting up libhogweed6t64:amd64 (3.10-1) ... (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 ... 6194 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.5-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-2) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.5-2) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6194 files and directories currently installed.) Preparing to unpack .../libunistring5_1.2-1_amd64.deb ... Unpacking libunistring5:amd64 (1.2-1) ... Setting up libunistring5:amd64 (1.2-1) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (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 ... 6200 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u3) ... Selecting previously unselected package libgnutls30t64: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 ... 6171 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.6-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.6-2) ... Setting up libgnutls30t64:amd64 (3.8.6-2) ... (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 ... 6200 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (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 ... 6200 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 ... 6200 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 ... 6201 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-6_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-6) over (1.0.8-5+b1) ... Setting up libbz2-1.0:amd64 (1.0.8-6) ... (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 ... 6200 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2+b1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2+b1) over (0.8.1-1) ... Setting up libxxhash0:amd64 (0.8.2-2+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 ... 6201 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-3_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-3) over (1.9.4-1) ... Setting up liblz4-1:amd64 (1.9.4-3) ... (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 ... 6201 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.2-2_amd64.deb ... Unpacking liblzma5:amd64 (5.6.2-2) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.6.2-2) ... (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 ... 6201 files and directories currently installed.) Preparing to unpack .../libudev1_256.7-2_amd64.deb ... Unpacking libudev1:amd64 (256.7-2) over (252.30-1~deb12u2) ... Setting up libudev1:amd64 (256.7-2) ... dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 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 ... 6201 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.6.1) ... Selecting previously unselected package libapt-pkg6.0t64: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 ... 6152 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.8_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.8) ... Setting up libapt-pkg6.0t64:amd64 (2.9.8) ... (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 ... 6198 files and directories currently installed.) Preparing to unpack .../tar_1.35+dfsg-3_amd64.deb ... Unpacking tar (1.35+dfsg-3) over (1.34+dfsg-1.2+deb12u1) ... Setting up tar (1.35+dfsg-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 ... 6199 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.11_amd64.deb ... Unpacking dpkg (1.22.11) over (1.21.22) ... Setting up dpkg (1.22.11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6186 files and directories currently installed.) Preparing to unpack .../findutils_4.10.0-3_amd64.deb ... Unpacking findutils (4.10.0-3) over (4.9.0-4) ... Setting up findutils (4.10.0-3) ... (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 ... 6184 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1.1_amd64.deb ... Unpacking gzip (1.12-1.1) over (1.12-1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1.1) ... (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 ... 6189 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64: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 ... 6183 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-9) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-9) ... (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 ... 6189 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-4_all.deb ... Unpacking libaudit-common (1:3.1.2-4) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-4) ... (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 ... 6189 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.5-2) ... (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 ... 6188 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-4+b1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-4+b1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-4+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 ... 6189 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-5) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-5) ... (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 ... 6189 files and directories currently installed.) Preparing to unpack .../perl-base_5.38.2-5_amd64.deb ... Unpacking perl-base (5.38.2-5) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-5) ... (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 ... 6193 files and directories currently installed.) Preparing to unpack .../debconf_1.5.87_all.deb ... Unpacking debconf (1.5.87) over (1.5.82) ... Setting up debconf (1.5.87) ... 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 ... 6192 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-7_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam0g:amd64 (1.5.3-7) ... (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 ... 6191 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4+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 ... 6192 files and directories currently installed.) Preparing to unpack .../libselinux1_3.7-3_amd64.deb ... Unpacking libselinux1:amd64 (3.7-3) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.7-3) ... (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 ... 6192 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-7) ... (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 ... 6191 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-7) ... Installing new version of config file /etc/security/namespace.init ... (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 ... 6191 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-7_all.deb ... Unpacking libpam-runtime (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-7) ... (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 ... 6190 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-9_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-9) over (1:4.13+dfsg1-1+b1) ... Setting up login (1:4.16.0-2+really2.40.2-9) ... Installing new version of config file /etc/pam.d/login ... (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 ... 6078 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.5-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.5-2) over (6.4-4) ... Setting up libtinfo6:amd64 (6.5-2) ... (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 ... 6078 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.5-2_amd64.deb ... Unpacking ncurses-bin (6.5-2) over (6.4-4) ... Setting up ncurses-bin (6.5-2) ... (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 ... 6078 files and directories currently installed.) 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 ... (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 ... 6078 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-9_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-9) over (2.38.1-5+deb12u1) ... Setting up libblkid1:amd64 (2.40.2-9) ... (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 ... 6079 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-9_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-9) over (2.38.1-5+deb12u1) ... Setting up libmount1:amd64 (2.40.2-9) ... (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 ... 6080 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-9_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-9) over (2.38.1-5+deb12u1) ... Setting up libsmartcols1:amd64 (2.40.2-9) ... (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 ... 6081 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-9_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-9) over (2.38.1-5+deb12u1) ... Setting up libuuid1:amd64 (2.40.2-9) ... (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 ... 6082 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-9_amd64.deb ... Unpacking util-linux (2.40.2-9) over (2.38.1-5+deb12u1) ... Setting up util-linux (2.40.2-9) ... (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 ... 6055 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.40.2-9_amd64.deb ... Adding 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-9) over (2.38.1-5+deb12u1) ... 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 dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux-extra (2.40.2-9) ... (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 ... 6094 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.272_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.272) over (0.270) ... Setting up libdebconfclient0:amd64 (0.272) ... (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 ... 6094 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.4_amd64.deb ... Unpacking base-passwd (3.6.4) over (3.6.1) ... Setting up base-passwd (3.6.4) ... (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 ... 6094 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-2) ... Selecting previously unselected package libbsd0: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 ... 6094 files and directories currently installed.) Preparing to unpack .../libbsd0_0.12.2-2_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-2) ... Setting up libbsd0:amd64 (0.12.2-2) ... (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 ... 6101 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-2_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-2) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-2) ... (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 ... 6101 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-2_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.2-2) over (1:2.5.1-4) ... Setting up libattr1:amd64 (1:2.5.2-2) ... (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 ... 6101 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.7-2_all.deb ... Unpacking libsemanage-common (3.7-2) over (3.4-1) ... Setting up libsemanage-common (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 ... 6100 files and directories currently installed.) Preparing to unpack .../libsepol2_3.7-1_amd64.deb ... Unpacking libsepol2:amd64 (3.7-1) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6100 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.7-2_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (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 ... 6099 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.16.0-4_amd64.deb ... Unpacking passwd (1:4.16.0-4) over (1:4.13+dfsg1-1+b1) ... Setting up passwd (1:4.16.0-4) ... (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 ... 6127 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) over (3.134) ... Setting up adduser (3.137) ... Installing new version of config file /etc/adduser.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 ... 6121 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.44-1_amd64.deb ... Unpacking gpgv (2.2.44-1) over (2.2.40-1.1) ... Setting up gpgv (2.2.44-1) ... (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 ... 6121 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.4_all.deb ... Unpacking debian-archive-keyring (2023.4) over (2023.3+deb12u1) ... Setting up debian-archive-keyring (2023.4) ... (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 ... 6121 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1+b1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1+b1) over (2.5.4-1+deb12u1) ... Setting up libseccomp2:amd64 (2.5.5-1+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 ... 6122 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (37~deb12u1) ... Setting up usr-is-merged (39) ... (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 ... 6122 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.67_all.deb ... Unpacking init-system-helpers (1.67) over (1.65.2) ... Setting up init-system-helpers (1.67) ... (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 ... 6122 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5-2_all.deb ... Unpacking ncurses-base (6.5-2) over (6.4-4) ... Setting up ncurses-base (6.5-2) ... (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 ... 6120 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.10-3_amd64.deb ... Unpacking sysvinit-utils (3.10-3) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.10-3) ... (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 ... 6120 files and directories currently installed.) Preparing to unpack .../logsave_1.47.1-1_amd64.deb ... Unpacking logsave (1.47.1-1) over (1.47.0-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 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 ... 6120 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2) ... Selecting previously unselected package libext2fs2t64: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 ... 6113 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.1-1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.1-1) ... (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 ... 6129 files and directories currently installed.) Preparing to unpack .../00-e2fsprogs_1.47.1-1_amd64.deb ... Unpacking e2fsprogs (1.47.1-1) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../01-mount_2.40.2-9_amd64.deb ... Unpacking mount (2.40.2-9) over (2.38.1-5+deb12u1) ... Preparing to unpack .../02-mawk_1.3.4.20240905-1_amd64.deb ... Unpacking mawk (1.3.4.20240905-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) over (2024a-0+deb12u1) ... Preparing to unpack .../04-gcc-12-base_12.4.0-2_amd64.deb ... Unpacking gcc-12-base:amd64 (12.4.0-2) over (12.2.0-14) ... Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) over (1.47.0-2) ... Preparing to unpack .../06-libedlib1_1.2.7-6_amd64.deb ... Unpacking libedlib1:amd64 (1.2.7-6) over (1.2.7-4+b1) ... Preparing to unpack .../07-libspoa7.0.0_4.1.4-2_amd64.deb ... Unpacking libspoa7.0.0:amd64 (4.1.4-2) over (4.0.8-1) ... Preparing to unpack .../08-libss2_1.47.1-1_amd64.deb ... Unpacking libss2:amd64 (1.47.1-1) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu': Directory not empty Preparing to unpack .../09-minimap2_2.27+dfsg-1+b1_amd64.deb ... Unpacking minimap2 (2.27+dfsg-1+b1) over (2.24+dfsg-3+b1) ... Preparing to unpack .../10-pinfish_0.1.0+ds-4+b2_amd64.deb ... Unpacking pinfish (0.1.0+ds-4+b2) over (0.1.0+ds-3) ... Setting up minimap2 (2.27+dfsg-1+b1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up gcc-12-base:amd64 (12.4.0-2) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 21 04:32:46 UTC 2024. Universal Time is now: Mon Oct 21 04:32:46 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libspoa7.0.0:amd64 (4.1.4-2) ... Setting up libss2:amd64 (1.47.1-1) ... Setting up logsave (1.47.1-1) ... Setting up pinfish (0.1.0+ds-4+b2) ... Setting up libedlib1:amd64 (1.2.7-6) ... Setting up mount (2.40.2-9) ... Setting up mawk (1.3.4.20240905-1) ... Setting up e2fsprogs (1.47.1-1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/mke2fs.conf ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for debianutils (5.20) ... 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.5s DUMP: ca111f865b2c758d894b83ca5485bf59 - 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m13.6s DUMP: Package: pinfish Source: pinfish (0.1.0+ds-4) Version: 0.1.0+ds-4+b2 Installed-Size: 8250 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), minimap2, racon Description-en: Collection of tools to annotate genomes using long read transcriptomics data The toolchain is composed of the following tools: 1. spliced_bam2gff - a tool for converting sorted BAM files containing spliced alignments into GFF2 format. Each read will be represented as a distinct transcript. This tool comes handy when visualizing spliced reads at particular loci and to provide input to the rest of the toolchain. . 2. cluster_gff - this tool takes a sorted GFF2 file as input and clusters together reads having similar exon/intron structure and creates a rough consensus of the clusters by taking the median of exon boundaries from all transcripts in the cluster. . 3. polish_clusters - this tool takes the cluster definitions generated by cluster_gff and for each cluster creates an error corrected read by mapping all reads on the read with the median length and polishing it using racon. The polished reads can be mapped to the genome using minimap2 or GMAP. . 4. collapse_partials - this tool takes GFFs generated by either cluster_gff or polish_clusters and filters out transcripts which are likely to be based on RNA degradation products from the 5' end. The tool clusters the input transcripts into "loci" by the 3' ends and discards transcripts which have a compatible transcripts in the loci with more exons. Description-md5: e070704f0ce179f7e25e747b54785f16 Homepage: https://github.com/nanoporetech/pinfish Built-Using: golang-1.23 (= 1.23.1-3), golang-github-biogo-biogo (= 1.0.4-1), golang-github-biogo-hts (= 1.4.5+dfsg1-1), golang-github-google-uuid (= 1.6.0-1) Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-4+b2_amd64.deb Size: 1408224 MD5sum: 4b1a59819affff06688681034b64cb0e SHA256: e18942da6b2ebd174a53f20132a401beced8318a2a3d7e49bc8ced951e5609a5 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m13.6s INFO: apt-cache knows about the following packages: pinfish 0m13.6s INFO: Running scripts pre_install 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m13.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m13.6s DUMP: pinfish: Installed: 0.1.0+ds-4+b2 Candidate: 0.1.0+ds-4+b2 Version table: *** 0.1.0+ds-4+b2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m13.9s DUMP: Reading package lists... Building dependency tree... Reading state information... pinfish is already the newest version (0.1.0+ds-4+b2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m13.9s INFO: Running scripts post_install 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m13.9s INFO: Running scripts post_distupgrade 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m14.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m14.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp_00_v2_z to sid 0m14.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m14.1s INFO: Running scripts pre_distupgrade 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m16.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7343 kB] Fetched 17.6 MB in 2s (11.4 MB/s) Reading package lists... 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'update'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m17.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt gcc-14-base libapt-pkg6.0t64 libaudit-common libaudit1 libcap-ng0 libgcc-s1 libstdc++6 perl-base pinfish tzdata 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6713 kB of archives. After this operation, 81.9 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-6 [1675 kB] Get:2 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-7 [46.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-7 [72.8 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-7 [713 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.9 [1045 kB] Get:6 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.9 [1413 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-3 [17.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:10 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:11 http://deb.debian.org/debian sid/main amd64 pinfish amd64 0.1.0+ds-4+b3 [1409 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6713 kB in 0s (19.4 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5345 files and directories currently installed.) Preparing to unpack .../perl-base_5.40.0-6_amd64.deb ... Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... Setting up perl-base (5.40.0-6) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14.2.0-7_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-7) over (14.2.0-6) ... Setting up gcc-14-base:amd64 (14.2.0-7) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-7_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-7) over (14.2.0-6) ... Setting up libgcc-s1:amd64 (14.2.0-7) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-7_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-7) over (14.2.0-6) ... Setting up libstdc++6:amd64 (14.2.0-7) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.9_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.9) over (2.9.8) ... Setting up libapt-pkg6.0t64:amd64 (2.9.9) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.9_amd64.deb ... Unpacking apt (2.9.9) over (2.9.8) ... Setting up apt (2.9.9) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-3_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-3) over (0.8.5-2) ... Setting up libcap-ng0:amd64 (0.8.5-3) ... (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 ... 5344 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.1-1) over (1:3.1.2-4+b1) ... Setting up libaudit1:amd64 (1:4.0.1-1) ... (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 ... 5343 files and directories currently installed.) Preparing to unpack .../tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) over (2024a-4) ... Preparing to unpack .../pinfish_0.1.0+ds-4+b3_amd64.deb ... Unpacking pinfish (0.1.0+ds-4+b3) over (0.1.0+ds-4+b2) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 21 04:32:51 UTC 2024. Universal Time is now: Mon Oct 21 04:32:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up pinfish (0.1.0+ds-4+b3) ... Processing triggers for libc-bin (2.40-3) ... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-yf', 'dist-upgrade'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.2s DUMP: bd3199b32d53dc12cf3fd24e43e269c6 - 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m18.3s DUMP: Package: pinfish Source: pinfish (0.1.0+ds-4) Version: 0.1.0+ds-4+b3 Installed-Size: 8254 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), minimap2, racon Description-en: Collection of tools to annotate genomes using long read transcriptomics data The toolchain is composed of the following tools: 1. spliced_bam2gff - a tool for converting sorted BAM files containing spliced alignments into GFF2 format. Each read will be represented as a distinct transcript. This tool comes handy when visualizing spliced reads at particular loci and to provide input to the rest of the toolchain. . 2. cluster_gff - this tool takes a sorted GFF2 file as input and clusters together reads having similar exon/intron structure and creates a rough consensus of the clusters by taking the median of exon boundaries from all transcripts in the cluster. . 3. polish_clusters - this tool takes the cluster definitions generated by cluster_gff and for each cluster creates an error corrected read by mapping all reads on the read with the median length and polishing it using racon. The polished reads can be mapped to the genome using minimap2 or GMAP. . 4. collapse_partials - this tool takes GFFs generated by either cluster_gff or polish_clusters and filters out transcripts which are likely to be based on RNA degradation products from the 5' end. The tool clusters the input transcripts into "loci" by the 3' ends and discards transcripts which have a compatible transcripts in the loci with more exons. Description-md5: e070704f0ce179f7e25e747b54785f16 Homepage: https://github.com/nanoporetech/pinfish Built-Using: golang-1.23 (= 1.23.2-1), golang-github-biogo-biogo (= 1.0.4-1), golang-github-biogo-hts (= 1.4.5+dfsg1-1), golang-github-google-uuid (= 1.6.0-1) Section: science Priority: optional Filename: pool/main/p/pinfish/pinfish_0.1.0+ds-4+b3_amd64.deb Size: 1408756 MD5sum: e3c4df4afb5753a53cd6edaa25b350aa SHA256: 63ec45bd2bc43fae3bd512deab8999df165cacbe24a07d37b7919ab8979975c9 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'show', '--no-all-versions', 'pinfish'] 0m18.3s INFO: apt-cache knows about the following packages: pinfish 0m18.3s INFO: Running scripts pre_install 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m18.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m18.4s DUMP: pinfish: Installed: 0.1.0+ds-4+b3 Candidate: 0.1.0+ds-4+b3 Version table: *** 0.1.0+ds-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m18.6s DUMP: Reading package lists... Building dependency tree... Reading state information... pinfish is already the newest version (0.1.0+ds-4+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish'] 0m18.6s INFO: Running scripts post_install 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m18.7s INFO: Running scripts post_distupgrade 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m18.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m18.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m19.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m19.1s INFO: Running scripts pre_install 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m19.1s 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: 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m19.1s DUMP: pinfish: Installed: 0.1.0+ds-4+b3 Candidate: 0.1.0+ds-4+b3 Version table: *** 0.1.0+ds-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-cache', 'policy', 'pinfish'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish=0.1.0+ds-4+b3'] 0m19.4s DUMP: Reading package lists... Building dependency tree... Reading state information... pinfish is already the newest version (0.1.0+ds-4+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', '-y', 'install', 'pinfish=0.1.0+ds-4+b3'] 0m19.4s INFO: Running scripts post_install 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_install_exceptions'] 0m19.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m19.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m19.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', '-ac', '--ignore-obsolete'] 0m20.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', '-ac', '--ignore-obsolete'] 0m20.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.1s DUMP: 0.15.6 0m20.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m20.1s INFO: Running adequate version 0.15.6 now. 0m20.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'pinfish'] 0m20.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'pinfish'] 0m20.2s INFO: Running scripts pre_remove 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_exceptions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/pre_remove_exceptions'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.6s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.9 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-7 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.9 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libedlib1:amd64 libedlib1 1.2.7-6 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libspoa7.0.0:amd64 libspoa7.0.0 4.1.4-2 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-7 install ok installed libsystemd0:amd64 libsystemd0 256.7-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.7-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed minimap2 minimap2 2.27+dfsg-1+b1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed pinfish pinfish 0.1.0+ds-4+b3 install ok installed racon racon 1.5.0-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-3 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed util-linux-extra util-linux-extra 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'remove', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'minimap2', 'racon', 'pinfish'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libedlib1 libspoa7.0.0 minimap2 pinfish racon 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. After this operation, 12.6 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 ... 5331 files and directories currently installed.) Removing pinfish (0.1.0+ds-4+b3) ... Removing racon (1.5.0-3) ... Removing libedlib1:amd64 (1.2.7-6) ... Removing libspoa7.0.0:amd64 (4.1.4-2) ... Removing minimap2 (2.27+dfsg-1+b1) ... Processing triggers for libc-bin (2.40-3) ... 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'remove', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'minimap2', 'racon', 'pinfish'] 0m21.0s INFO: Running scripts post_remove 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_remove_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_remove_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'minimap2', 'racon'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove libedlib1 which isn't installed dpkg: warning: ignoring request to remove libspoa7.0.0 which isn't installed dpkg: warning: ignoring request to remove minimap2 which isn't installed dpkg: warning: ignoring request to remove racon which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', 'libedlib1:amd64', 'libspoa7.0.0:amd64', 'minimap2', 'racon'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', 'pinfish'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove pinfish which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', 'pinfish'] 0m21.0s INFO: Running scripts post_purge 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--remove', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg', '--remove', '--pending'] 0m21.0s INFO: Running scripts post_test 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m21.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-divert', '--list'] 0m21.2s DUMP: diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'dpkg-divert', '--list'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'clean'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z', 'apt-get', 'clean'] 0m21.3s DEBUG: Recording chroot state 0m21.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/shm'] 0m21.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/shm'] 0m21.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/console'] 0m21.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/console'] 0m21.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/ptmx'] 0m21.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/ptmx'] 0m21.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts'] 0m21.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/dev/pts'] 0m21.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/proc'] 0m21.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z/proc'] 0m21.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m22.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_00_v2_z'] 0m22.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_00_v2_z 0m22.0s INFO: PASS: Upgrading between Debian distributions. 0m22.0s INFO: PASS: All tests. 0m22.0s INFO: piuparts run ends. ret=0 End: 2024-10-21 04:32:56 GMT