Start: 2024-11-07 15:21:56 GMT [testing] Package: pigx-rnaseq Version: 0.1.1-1 Installed-Size: 176 Maintainer: Debian Med Packaging Team Architecture: all Depends: fastp, fastqc, hisat2 | rna-star, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3:any, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt, r-cran-ggplot2, r-cran-ggpubr, r-cran-ggrepel, r-cran-gprofiler2, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore Recommends: hisat2, rna-star Description: pipeline for checkpointed and distributed RNA-seq analyses Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Description-md5: e48b7ff1eb2b189a5bedb2ce0c32035c Section: science Priority: optional Filename: pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.1-1_all.deb Size: 61696 MD5sum: 31284ff2cec66262fab4b45074a1c1ad SHA256: 286ce30816f15c9348617ee7aa74d60a29c39d94b0942b330eee7df942b6192a [sid] Package: pigx-rnaseq Version: 0.1.1-1 Installed-Size: 176 Maintainer: Debian Med Packaging Team Architecture: all Depends: fastp, fastqc, hisat2 | rna-star, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3:any, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt, r-cran-ggplot2, r-cran-ggpubr, r-cran-ggrepel, r-cran-gprofiler2, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore Recommends: hisat2, rna-star Description: pipeline for checkpointed and distributed RNA-seq analyses Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Description-md5: e48b7ff1eb2b189a5bedb2ce0c32035c Section: science Priority: optional Filename: pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.1-1_all.deb Size: 61696 MD5sum: 31284ff2cec66262fab4b45074a1c1ad SHA256: 286ce30816f15c9348617ee7aa74d60a29c39d94b0942b330eee7df942b6192a 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt pigx-rnaseq=0.1.1-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt pigx-rnaseq=0.1.1-1 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/tmpdmez5w6x 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpdmez5w6x 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/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/tmpdmez5w6x/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/tmpdmez5w6x/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie 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/tmpdmez5w6x/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9341 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6241 kB] Fetched 15.8 MB in 1s (18.3 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: coreutils libssl3t64 libsystemd0 libudev1 openssl-provider-legacy 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6019 kB of archives. After this operation, 296 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.7-3 [382 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.7-3 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6019 kB in 0s (92.7 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 ... 5166 files and directories currently installed.) Preparing to unpack .../coreutils_9.5-1+b1_amd64.deb ... Unpacking coreutils (9.5-1+b1) over (9.4-3.1) ... Setting up coreutils (9.5-1+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 ... 5167 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.3.2-2_amd64.deb ... Unpacking openssl-provider-legacy (3.3.2-2) over (3.3.2-1) ... Setting up openssl-provider-legacy (3.3.2-2) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.3.2-2_amd64.deb ... Unpacking libssl3t64:amd64 (3.3.2-2) over (3.3.2-1) ... Setting up libssl3t64:amd64 (3.3.2-2) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libsystemd0_256.7-3_amd64.deb ... Unpacking libsystemd0:amd64 (256.7-3) over (256.7-2) ... Setting up libsystemd0:amd64 (256.7-3) ... (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 ... 5167 files and directories currently installed.) Preparing to unpack .../libudev1_256.7-3_amd64.deb ... Unpacking libudev1:amd64 (256.7-3) over (256.7-2) ... Setting up libudev1:amd64 (256.7-3) ... Processing triggers for libc-bin (2.40-3) ... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: 656961bed45e71a26979cb287e562a45 - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s 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' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 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 9.5-1+b1 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+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-6 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+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 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+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 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+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 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 libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 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+b1 install ok installed mawk mawk 1.3.4.20240905-1 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+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_test_exceptions'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_test_root_password'] 0m3.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_test_root_password'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 0m3.4s DUMP: Package: pigx-rnaseq Version: 0.1.1-1 Installed-Size: 176 Maintainer: Debian Med Packaging Team Architecture: all Depends: fastp, fastqc, hisat2 | rna-star, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3:any, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt, r-cran-ggplot2, r-cran-ggpubr, r-cran-ggrepel, r-cran-gprofiler2, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore Recommends: hisat2, rna-star Description-en: pipeline for checkpointed and distributed RNA-seq analyses This package provides a automated workflow for the automated analysis of RNA-seq experiments. A series of well-accecpted tools are connected in Python scripts and controlled via snakemake. This supports the parallel execution of these workflows and provides checkpointing, such that interrupted workflows can take up their work again. Description-md5: e48b7ff1eb2b189a5bedb2ce0c32035c Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Section: science Priority: optional Filename: pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.1-1_all.deb Size: 61696 MD5sum: 31284ff2cec66262fab4b45074a1c1ad SHA256: 286ce30816f15c9348617ee7aa74d60a29c39d94b0942b330eee7df942b6192a 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 0m3.4s INFO: apt-cache knows about the following packages: pigx-rnaseq 0m3.4s INFO: Running scripts pre_install 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 0m3.5s 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: 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 0m3.5s DUMP: pigx-rnaseq: Installed: (none) Candidate: 0.1.1-1 Version table: 0.1.1-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 2m0.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser adwaita-icon-theme at-spi2-common blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cutadapt dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libapache-pom-java libapparmor1 libasan8 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0t64 libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcloudproviders0 libcolord2 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu72 libimagequant0 libisal2 libitm1 libjbig0 libjbzip2-java libjemalloc2 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-metadata libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnsl2 libnspr4 libnss3 libnuma1 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev littler media-types megadepth mesa-libgallium multiqc ncbi-vdb-data netbase node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre openjdk-21-jre-headless openssl pandoc pandoc-data perl perl-modules-5.40 pigz procps python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-appdirs python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-defusedxml python3-dnaio python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-fs python3-git python3-gitdb python3-htseq python3-humanfriendly python3-humanize python3-idna python3-imagesize python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-matplotlib python3-mdurl python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-plotly python3-psutil python3-pulp python3-py python3-py2bit python3-pyaml-env python3-pybigwig python3-pygments python3-pyparsing python3-pysam python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yte python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tximport r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-backports r-cran-base64enc r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-boot r-cran-broom r-cran-bslib r-cran-cachem r-cran-car r-cran-cardata r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr r-cran-clock r-cran-codetools r-cran-colorspace r-cran-colourpicker r-cran-commonmark r-cran-conquer r-cran-corrplot r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-data.table r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby r-cran-dplyr r-cran-dt r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-forcats r-cran-foreach r-cran-foreign r-cran-formatr r-cran-formula r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-ggpubr r-cran-ggrepel r-cran-ggsci r-cran-ggsignif r-cran-globals r-cran-glue r-cran-gower r-cran-gprofiler2 r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lava r-cran-lazyeval r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lme4 r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-openssl r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest r-cran-pheatmap r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plotly r-cran-plyr r-cran-polynom r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstatix r-cran-sass r-cran-scales r-cran-shape r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev Suggested packages: liblocale-gettext-perl cron quota adwaita-icon-theme-legacy blt-demo gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn apache2 | lighttpd | httpd alsa-utils libasound2-plugins libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libc-devtools glibc-doc manpages-dev colord libasm-java libxz-java libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common gdbm-l10n low-memory-monitor krb5-doc krb5-user gvfs picard-tools libhwloc-contrib-plugins libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc liblcms2-utils libngs-java-doc libcryptsetup12 libtss2-rc0t64 pciutils pcscd rhino lm-sensors libstdc++-14-doc libarchive13t64 libbpf1 libdw1t64 libfido2-1 libip4tc2 libpwquality1 libqrencode4 tcl8.6 tk8.6 r-bioc-megadepth nodejs libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex citation-style-language-styles perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-venv python-attr-doc python-charset-normalizer-doc python-cycler-doc python-python-deeptoolsintervals-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base python-fastjsonschema-doc python-git-doc python-jinja2-doc python-jsonschema-doc python3-pip python-lxml-doc python-markdown-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils python-mpmath-doc python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc python3-setuptools python3-pandas python3-ipykernel subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python3-azure python3-azure-storage python3-stemmer dvisvgm fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic python-sympy-doc python-tenacity-doc tix python3-tk-dbg python-traitlets-doc python3.12-venv python3.12-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-golubesets r-bioc-biocstyle r-bioc-limma r-bioc-annotationdbi r-bioc-affy r-bioc-annotate r-cran-testthat r-cran-bbmisc r-cran-doparallel r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-bioc-pwalign r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-tximeta r-bioc-tximportdata r-cran-pbapply r-bioc-glmgampoi r-cran-biocmanager r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-keggrest r-bioc-sparsematrixstats r-bioc-org.hs.eg.db r-bioc-graph r-bioc-rhdf5 r-cran-dbi r-cran-rmariadb r-cran-roxygen2 r-cran-ff r-cran-bradleyterry2 r-cran-covr r-cran-ellipse r-cran-gam r-cran-mlbench r-cran-party r-cran-pls r-cran-randomforest r-cran-rann r-cran-rstudioapi r-cran-ragg r-cran-vdiffr r-cran-tinytest r-cran-magick r-cran-sf r-cran-getopt r-cran-interp r-cran-multcomp r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-here r-cran-pkgbuild r-cran-pkgload r-cran-plm r-cran-zoo readline-doc cwltool sgml-base-doc slurm-client snakemake-doc systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd debhelper Recommended packages: librsvg2-common patch less ssh-client python3-hisat2 bcftools alsa-ucm-conf alsa-topology-conf at-spi2-core curl manpages manpages-dev libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin libhwloc-plugins node-jquery libjson-xs-perl krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libkmod2 mesa-vulkan-drivers | vulkan-icd node-clipboard libjs-filesaver texlive-xetex libatk-wrapper-java-jni fonts-dejavu-extra rna-star psmisc linux-sysctl-defaults python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-cssselect python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-olefile g++ | c++-compiler python3-boto3 python3-paramiko python3-zstandard make isympy-common r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-aer r-cran-bbmle r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-geepack r-cran-glmnet r-cran-gmm r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks r-cran-lavaan r-cran-leaps r-cran-lmtest r-cran-lsmeans r-cran-maps r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network r-cran-ordinal r-cran-plm r-cran-psych r-cran-robust r-cran-robustbase r-cran-rsample r-cran-sandwich r-cran-spdep r-cran-spatialreg r-cran-spelling r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-thematic r-cran-earth r-cran-mda r-cran-mlmetrics r-cran-fastica r-cran-kernlab r-cran-themis r-cran-callr r-cran-mockery r-cran-processx r-cran-ps r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-slider r-cran-mvtnorm r-cran-vcd r-cran-png r-cran-jpeg r-cran-viridis r-cran-xml2 r-cran-seriation r-cran-cairo r-cran-gridgraphics r-cran-magick r-cran-patchwork r-cran-ragg r-cran-vdiffr r-cran-venndiagram r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-webutils r-cran-xts r-cran-markdown r-cran-dbi r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-testit w3m | www-browser r-cran-unitizer r-cran-rsvg r-cran-rhpcblasctl r-cran-r.rsp r-cran-pkgload r-cran-hexbin r-cran-mapproj r-cran-profvis r-cran-sf r-cran-svglite r-cran-devtools r-cran-ggbeeswarm r-cran-waldo r-cran-roxygen2 r-cran-usethis r-cran-mlbench r-cran-th.data r-cran-randomforest r-cran-party r-cran-gridsvg r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-webshot node-highlight.js r-cran-ellipse r-cran-fields r-bioc-graph r-cran-bookdown r-cran-igraph r-cran-lavasearch2 r-cran-mets r-cran-optimx r-cran-polycor r-cran-lintr r-cran-tidyverse r-cran-r.devices r-cran-sodium r-cran-ggthemes r-cran-ggally r-cran-ggalluvial r-cran-dendextend r-cran-irdisplay r-cran-palmerpenguins r-cran-rversions r-cran-doparallel r-cran-itertools r-cran-logcondens r-cran-pbmcapply r-cran-furrr r-cran-cba r-cran-ddalpha r-cran-dials r-cran-rann r-cran-rcpproll r-cran-rspectra r-cran-splines2 r-cran-rcppml r-cran-dimred r-cran-runit r-cran-dygraphs r-cran-rsconnect r-cran-downlit r-cran-coin r-cran-dichromat r-cran-setrng r-cran-mockr r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-remotes r-cran-renv cwltool imagemagick python3-yappi python3-azure-storage python3-biopython python3-botocore python3-dropbox python3-flask python3-ftputil python3-irodsclient python3-kubernetes systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adduser adwaita-icon-theme at-spi2-common blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cutadapt dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libapache-pom-java libapparmor1 libasan8 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0t64 libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcloudproviders0 libcolord2 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu72 libimagequant0 libisal2 libitm1 libjbig0 libjbzip2-java libjemalloc2 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-metadata libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmjson-java libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnsl2 libnspr4 libnss3 libnuma1 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev littler media-types megadepth mesa-libgallium multiqc ncbi-vdb-data netbase node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre openjdk-21-jre-headless openssl pandoc pandoc-data perl perl-modules-5.40 pigx-rnaseq pigz procps python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-appdirs python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-defusedxml python3-dnaio python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-fs python3-git python3-gitdb python3-htseq python3-humanfriendly python3-humanize python3-idna python3-imagesize python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-matplotlib python3-mdurl python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-plotly python3-psutil python3-pulp python3-py python3-py2bit python3-pyaml-env python3-pybigwig python3-pygments python3-pyparsing python3-pysam python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yte python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tximport r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-backports r-cran-base64enc r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-boot r-cran-broom r-cran-bslib r-cran-cachem r-cran-car r-cran-cardata r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr r-cran-clock r-cran-codetools r-cran-colorspace r-cran-colourpicker r-cran-commonmark r-cran-conquer r-cran-corrplot r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-data.table r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby r-cran-dplyr r-cran-dt r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-forcats r-cran-foreach r-cran-foreign r-cran-formatr r-cran-formula r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-ggpubr r-cran-ggrepel r-cran-ggsci r-cran-ggsignif r-cran-globals r-cran-glue r-cran-gower r-cran-gprofiler2 r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lava r-cran-lazyeval r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lme4 r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-openssl r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest r-cran-pheatmap r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plotly r-cran-plyr r-cran-polynom r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstatix r-cran-sass r-cran-scales r-cran-shape r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev 0 upgraded, 651 newly installed, 0 to remove and 0 not upgraded. Need to get 587 MB of archives. After this operation, 2206 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-1+b2 [42.1 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 256.7-3 [2068 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 256.7-3 [3492 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 256.7-3 [58.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-6 [203 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.14.10-6 [106 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-6 [79.2 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.14.10-6 [185 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-6 [80.2 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.14.10-6 [98.5 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-6 [3022 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-6 [4326 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-6 [267 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:28 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:39 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 256.7-3 [280 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-6 [9284 B] Get:50 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.16.3+ds-2 [50.1 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.54.0-1 [170 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b2 [804 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:87 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-6 [836 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-1+b1 [459 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-1+b1 [293 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:105 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 python3-dnaio amd64 1.2.2-1 [83.4 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 python3-cutadapt amd64 4.7-2+b1 [188 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 cutadapt all 4.7-2 [25.1 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-6 [79.0 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b3 [41.9 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b3 [32.6 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b3 [28.8 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get:116 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.105-2 [1393 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.0-2 [55.8 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB] Get:121 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:122 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b3 [112 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b3 [43.2 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b3 [47.5 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get:151 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b2 [16.0 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b2 [111 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b1 [36.3 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:163 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.4-1 [37.9 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b2 [232 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get:174 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.3-1 [26.0 MB] Get:183 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.4-1 [9182 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.4-1 [42.7 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.4-1 [43.8 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.4-1 [154 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.12-1+b1 [371 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b2 [25.9 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [205 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:199 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libisal2 amd64 2.31.0-0.3 [114 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 fastp amd64 0.23.4+dfsg-1 [203 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get:206 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.17.0-1 [488 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-9 [155 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-9 [23.8 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-9 [110 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.5-2 [6396 B] Get:224 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 fastqc all 0.12.1+dfsg-4 [398 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 git-man all 1:2.45.2-1 [2158 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 git amd64 1:2.45.2-1 [8645 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 hisat2 amd64 2.2.1-5 [3702 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:248 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-6 [2729 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 libbigwig0t64 amd64 0.4.7+dfsg-3.1+b2 [28.7 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-6 [137 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-6 [25.9 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-6 [1205 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-6 [2461 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-6 [1075 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-6 [1489 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-6 [145 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-6 [2672 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.11.5-1 [2443 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-3 [1956 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-6 [2367 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get:265 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:266 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.2 [281 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3.2 [253 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2 [347 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.10.1-2 [352 kB] Get:270 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-2+b2 [275 kB] Get:276 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:277 http://deb.debian.org/debian trixie/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:278 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:279 http://deb.debian.org/debian trixie/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:280 http://deb.debian.org/debian trixie/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:281 http://deb.debian.org/debian trixie/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:282 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:283 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:284 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get:285 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get:286 http://deb.debian.org/debian trixie/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:287 http://deb.debian.org/debian trixie/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:288 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:289 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get:290 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:291 http://deb.debian.org/debian trixie/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:292 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:293 http://deb.debian.org/debian trixie/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:294 http://deb.debian.org/debian trixie/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:295 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:296 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get:297 http://deb.debian.org/debian trixie/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:298 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:299 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:300 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.6-3+b2 [147 kB] Get:301 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get:302 http://deb.debian.org/debian trixie/main amd64 libnlopt0 amd64 2.7.1-5+b5 [178 kB] Get:303 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:304 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:305 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:306 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:307 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get:308 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:309 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:310 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:311 http://deb.debian.org/debian trixie/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get:312 http://deb.debian.org/debian trixie/main amd64 libtbbmalloc2 amd64 2021.12.0-1 [48.9 kB] Get:313 http://deb.debian.org/debian trixie/main amd64 libtbbbind-2-5 amd64 2021.12.0-1 [14.4 kB] Get:314 http://deb.debian.org/debian trixie/main amd64 libtbb12 amd64 2021.12.0-1 [87.8 kB] Get:315 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get:316 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:317 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:318 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:319 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:320 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get:321 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:322 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:323 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:324 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get:325 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:326 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:327 http://deb.debian.org/debian trixie/main amd64 megadepth amd64 1.2.0-4+b1 [83.0 kB] Get:328 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:329 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.1.7-2 [94.3 kB] Get:330 http://deb.debian.org/debian trixie/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:331 http://deb.debian.org/debian trixie/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:332 http://deb.debian.org/debian trixie/main amd64 python3-humanize all 4.11.0-1 [52.7 kB] Get:333 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get:334 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get:335 http://deb.debian.org/debian trixie/main amd64 python3-markdown all 3.7-1 [85.1 kB] Get:336 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:337 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:338 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get:339 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.6-1 [112 kB] Get:340 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-1 [103 kB] Get:341 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.6-1 [9428 B] Get:342 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1 [79.4 kB] Get:343 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:344 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:345 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2 [215 kB] Get:346 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:347 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b5 [318 kB] Get:348 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:349 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get:350 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:351 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:352 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1 [1251 kB] Get:353 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b4 [25.2 kB] Get:354 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:355 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get:356 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:357 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:358 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:359 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:360 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b2 [298 kB] Get:361 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:362 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4 [1429 kB] Get:363 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2 [60.9 kB] Get:364 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:365 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3 [5560 kB] Get:366 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:367 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1 [118 kB] Get:368 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:369 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:370 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:371 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:372 http://deb.debian.org/debian trixie/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get:373 http://deb.debian.org/debian trixie/main amd64 python3-rpds-py amd64 0.20.1-1 [252 kB] Get:374 http://deb.debian.org/debian trixie/main amd64 python3-referencing all 0.35.1-1 [23.5 kB] Get:375 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:376 http://deb.debian.org/debian trixie/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get:377 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:378 http://deb.debian.org/debian trixie/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:379 http://deb.debian.org/debian trixie/main amd64 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get:380 http://deb.debian.org/debian trixie/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get:381 http://deb.debian.org/debian trixie/main amd64 python3-tenacity all 8.4.2+really8.4.1-1 [46.0 kB] Get:382 http://deb.debian.org/debian trixie/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get:383 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get:384 http://deb.debian.org/debian trixie/main amd64 python3-pyaml-env all 1.2.1-2 [9032 B] Get:385 http://deb.debian.org/debian trixie/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get:386 http://deb.debian.org/debian trixie/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get:387 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get:388 http://deb.debian.org/debian trixie/main amd64 python3-rich all 13.7.1-1 [201 kB] Get:389 http://deb.debian.org/debian trixie/main amd64 python3-rich-click all 1.6.0-1 [20.8 kB] Get:390 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get:391 http://deb.debian.org/debian trixie/main amd64 python3-colormath all 3.0.0-4 [34.7 kB] Get:392 http://deb.debian.org/debian trixie/main amd64 python3-spectra all 0.0.11-4 [16.5 kB] Get:393 http://deb.debian.org/debian trixie/main amd64 python3-lzstring all 1.0.4-3 [5544 B] Get:394 http://deb.debian.org/debian trixie/main amd64 multiqc all 1.21+dfsg-2 [781 kB] Get:395 http://deb.debian.org/debian trixie/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:396 http://deb.debian.org/debian trixie/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:397 http://deb.debian.org/debian trixie/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:398 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:399 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get:400 http://deb.debian.org/debian trixie/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b9 [50.9 kB] Get:401 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get:402 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get:403 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get:404 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get:405 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.14.0-1 [111 kB] Get:406 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get:407 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:408 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:409 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get:410 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get:411 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:412 http://deb.debian.org/debian trixie/main amd64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get:413 http://deb.debian.org/debian trixie/main amd64 python3-py2bit amd64 0.3.1-3+b1 [19.1 kB] Get:414 http://deb.debian.org/debian trixie/main amd64 python3-pybigwig amd64 0.3.23+dfsg-1 [38.7 kB] Get:415 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:416 http://deb.debian.org/debian trixie/main amd64 python3-deeptools all 3.5.5+dfsg-1 [149 kB] Get:417 http://deb.debian.org/debian trixie/main amd64 python3-htseq amd64 2.0.5-2+b1 [309 kB] Get:418 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:419 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:420 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:421 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:422 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:423 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:424 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:425 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:426 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:427 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:428 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:429 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:430 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:431 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:432 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:433 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:434 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:435 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1842 kB] Get:436 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:437 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:438 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:439 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:440 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:441 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:442 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:443 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:444 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:445 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:446 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:447 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:448 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:449 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:450 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:451 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:452 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:453 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:454 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:455 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:456 http://deb.debian.org/debian trixie/main amd64 r-cran-locfit amd64 1.5-9.10-1 [515 kB] Get:457 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:458 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:459 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:460 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:461 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:462 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:463 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get:464 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:465 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:466 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:467 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:468 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:469 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:470 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:471 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:472 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:473 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:474 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:475 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:476 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:477 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:478 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:479 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:480 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:481 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:482 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:483 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:484 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpparmadillo amd64 14.0.2-1-1 [863 kB] Get:485 http://deb.debian.org/debian trixie/main amd64 r-bioc-deseq2 amd64 1.44.0+dfsg-1 [1283 kB] Get:486 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:487 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:488 http://deb.debian.org/debian trixie/main amd64 r-cran-bitops amd64 1.0-8-1 [30.7 kB] Get:489 http://deb.debian.org/debian trixie/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:490 http://deb.debian.org/debian trixie/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:491 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:492 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:493 http://deb.debian.org/debian trixie/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:494 http://deb.debian.org/debian trixie/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:495 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:496 http://deb.debian.org/debian trixie/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:497 http://deb.debian.org/debian trixie/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:498 http://deb.debian.org/debian trixie/main amd64 r-bioc-tximport all 1.32.0+dfsg-1 [91.2 kB] Get:499 http://deb.debian.org/debian trixie/main amd64 r-cran-corrplot all 0.94-1 [134 kB] Get:500 http://deb.debian.org/debian trixie/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:501 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:502 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:503 http://deb.debian.org/debian trixie/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:504 http://deb.debian.org/debian trixie/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get:505 http://deb.debian.org/debian trixie/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:506 http://deb.debian.org/debian trixie/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:507 http://deb.debian.org/debian trixie/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:508 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:509 http://deb.debian.org/debian trixie/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:510 http://deb.debian.org/debian trixie/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:511 http://deb.debian.org/debian trixie/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get:512 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:513 http://deb.debian.org/debian trixie/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:514 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:515 http://deb.debian.org/debian trixie/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:516 http://deb.debian.org/debian trixie/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:517 http://deb.debian.org/debian trixie/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:518 http://deb.debian.org/debian trixie/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:519 http://deb.debian.org/debian trixie/main amd64 r-cran-shiny all 1.9.1+dfsg-1 [3126 kB] Get:520 http://deb.debian.org/debian trixie/main amd64 r-cran-crosstalk all 1.2.1+dfsg-1 [175 kB] Get:521 http://deb.debian.org/debian trixie/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:522 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get:523 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.48+dfsg-1 [544 kB] Get:524 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:525 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.48+dfsg-1 [912 kB] Get:526 http://deb.debian.org/debian trixie/main amd64 r-cran-tinytex all 0.53-1 [146 kB] Get:527 http://deb.debian.org/debian trixie/main amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1474 kB] Get:528 http://deb.debian.org/debian trixie/main amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] Get:529 http://deb.debian.org/debian trixie/main amd64 r-cran-dt all 0.33+dfsg-1 [248 kB] Get:530 http://deb.debian.org/debian trixie/main amd64 r-cran-ggrepel amd64 0.9.5-2 [251 kB] Get:531 http://deb.debian.org/debian trixie/main amd64 r-cran-ggsci all 3.2.0-1 [2103 kB] Get:532 http://deb.debian.org/debian trixie/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:533 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:534 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:535 http://deb.debian.org/debian trixie/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:536 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get:537 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:538 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:539 http://deb.debian.org/debian trixie/main amd64 r-cran-cowplot all 1.1.3+dfsg-1 [638 kB] Get:540 http://deb.debian.org/debian trixie/main amd64 r-cran-ggsignif all 0.6.4-1 [589 kB] Get:541 http://deb.debian.org/debian trixie/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:542 http://deb.debian.org/debian trixie/main amd64 r-cran-polynom all 1.4-1+dfsg-1 [92.5 kB] Get:543 http://deb.debian.org/debian trixie/main amd64 r-cran-backports amd64 1.5.0-2 [121 kB] Get:544 http://deb.debian.org/debian trixie/main amd64 r-cran-broom all 1.0.7+dfsg-1 [1846 kB] Get:545 http://deb.debian.org/debian trixie/main amd64 r-cran-cardata all 3.0.5-1 [1797 kB] Get:546 http://deb.debian.org/debian trixie/main amd64 r-cran-formula all 1.2-5-1 [158 kB] Get:547 http://deb.debian.org/debian trixie/main amd64 r-cran-nnet amd64 7.3-19-2 [111 kB] Get:548 http://deb.debian.org/debian trixie/main amd64 r-cran-boot all 1.3-31-1 [639 kB] Get:549 http://deb.debian.org/debian trixie/main amd64 r-cran-minqa amd64 1.2.8-1 [118 kB] Get:550 http://deb.debian.org/debian trixie/main amd64 r-cran-nloptr amd64 2.1.1-1 [256 kB] Get:551 http://deb.debian.org/debian trixie/main amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1411 kB] Get:552 http://deb.debian.org/debian trixie/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:553 http://deb.debian.org/debian trixie/main amd64 r-cran-lme4 amd64 1.1-35.5-1 [4126 kB] Get:554 http://deb.debian.org/debian trixie/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get:555 http://deb.debian.org/debian trixie/main amd64 r-cran-deriv all 4.1.6-1 [151 kB] Get:556 http://deb.debian.org/debian trixie/main amd64 r-cran-modelr all 0.1.11-1 [204 kB] Get:557 http://deb.debian.org/debian trixie/main amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.1 kB] Get:558 http://deb.debian.org/debian trixie/main amd64 r-cran-doby all 4.6.24-1 [4777 kB] Get:559 http://deb.debian.org/debian trixie/main amd64 r-cran-pbkrtest all 0.5.3-1 [180 kB] Get:560 http://deb.debian.org/debian trixie/main amd64 r-cran-sparsem amd64 1.84-2-1+b1 [794 kB] Get:561 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixmodels all 0.5-3-1 [364 kB] Get:562 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.7-0-1 [6305 kB] Get:563 http://deb.debian.org/debian trixie/main amd64 r-cran-class amd64 7.3-22-2 [87.3 kB] Get:564 http://deb.debian.org/debian trixie/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] Get:565 http://deb.debian.org/debian trixie/main amd64 r-cran-e1071 amd64 1.7-16-1 [562 kB] Get:566 http://deb.debian.org/debian trixie/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:567 http://deb.debian.org/debian trixie/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:568 http://deb.debian.org/debian trixie/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB] Get:569 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:570 http://deb.debian.org/debian trixie/main amd64 r-cran-proc amd64 1.18.5-1 [987 kB] Get:571 http://deb.debian.org/debian trixie/main amd64 r-cran-tzdb amd64 0.4.0-2 [499 kB] Get:572 http://deb.debian.org/debian trixie/main amd64 r-cran-clock amd64 0.7.1-1 [1784 kB] Get:573 http://deb.debian.org/debian trixie/main amd64 r-cran-gower amd64 1.0.1-1 [207 kB] Get:574 http://deb.debian.org/debian trixie/main amd64 r-cran-hardhat all 1.4.0+dfsg-1 [668 kB] Get:575 http://deb.debian.org/debian trixie/main amd64 r-cran-rpart amd64 4.1.23-1 [685 kB] Get:576 http://deb.debian.org/debian trixie/main amd64 r-cran-shape all 1.4.6.1-1 [752 kB] Get:577 http://deb.debian.org/debian trixie/main amd64 r-cran-diagram all 1.6.5-2 [656 kB] Get:578 http://deb.debian.org/debian trixie/main amd64 r-cran-kernsmooth amd64 2.23-24-1 [92.7 kB] Get:579 http://deb.debian.org/debian trixie/main amd64 r-cran-globals all 0.16.3-1 [120 kB] Get:580 http://deb.debian.org/debian trixie/main amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] Get:581 http://deb.debian.org/debian trixie/main amd64 r-cran-parallelly amd64 1.38.0-1 [388 kB] Get:582 http://deb.debian.org/debian trixie/main amd64 r-cran-future all 1.34.0+dfsg-1 [649 kB] Get:583 http://deb.debian.org/debian trixie/main amd64 r-cran-future.apply all 1.11.2+dfsg-1 [172 kB] Get:584 http://deb.debian.org/debian trixie/main amd64 r-cran-progressr all 0.14.0-1 [337 kB] Get:585 http://deb.debian.org/debian trixie/main amd64 r-cran-squarem all 2021.1-1 [179 kB] Get:586 http://deb.debian.org/debian trixie/main amd64 r-cran-lava all 1.7.3+dfsg-1 [2207 kB] Get:587 http://deb.debian.org/debian trixie/main amd64 r-cran-prodlim amd64 2024.06.25-1 [416 kB] Get:588 http://deb.debian.org/debian trixie/main amd64 r-cran-ipred amd64 0.9-15-1 [387 kB] Get:589 http://deb.debian.org/debian trixie/main amd64 r-cran-timechange amd64 0.3.0-1 [173 kB] Get:590 http://deb.debian.org/debian trixie/main amd64 r-cran-lubridate amd64 1.9.3+dfsg-1 [1018 kB] Get:591 http://deb.debian.org/debian trixie/main amd64 r-cran-timedate amd64 4041.110-1 [1211 kB] Get:592 http://deb.debian.org/debian trixie/main amd64 r-cran-recipes all 1.1.0+dfsg-1 [2047 kB] Get:593 http://deb.debian.org/debian trixie/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:594 http://deb.debian.org/debian trixie/main amd64 r-cran-caret amd64 6.0-94+dfsg-1 [3446 kB] Get:595 http://deb.debian.org/debian trixie/main amd64 r-cran-conquer amd64 1.3.3-1 [471 kB] Get:596 http://deb.debian.org/debian trixie/main amd64 r-cran-quantreg amd64 5.99-1 [1544 kB] Get:597 http://deb.debian.org/debian trixie/main amd64 r-cran-foreign amd64 0.8.87-1 [253 kB] Get:598 http://deb.debian.org/debian trixie/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:599 http://deb.debian.org/debian trixie/main amd64 r-cran-forcats all 1.0.0-1 [413 kB] Get:600 http://deb.debian.org/debian trixie/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:601 http://deb.debian.org/debian trixie/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:602 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:603 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:604 http://deb.debian.org/debian trixie/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:605 http://deb.debian.org/debian trixie/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:606 http://deb.debian.org/debian trixie/main amd64 r-cran-vroom amd64 1.6.5-1 [830 kB] Get:607 http://deb.debian.org/debian trixie/main amd64 r-cran-readr amd64 2.1.5-1 [759 kB] Get:608 http://deb.debian.org/debian trixie/main amd64 r-cran-haven amd64 2.5.4-1 [342 kB] Get:609 http://deb.debian.org/debian trixie/main amd64 r-cran-rematch all 2.0.0-1 [18.2 kB] Get:610 http://deb.debian.org/debian trixie/main amd64 r-cran-cellranger all 1.1.0-3 [100 kB] Get:611 http://deb.debian.org/debian trixie/main amd64 r-cran-readxl amd64 1.4.3-1 [723 kB] Get:612 http://deb.debian.org/debian trixie/main amd64 r-cran-writexl amd64 1.5.1-1 [147 kB] Get:613 http://deb.debian.org/debian trixie/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get:614 http://deb.debian.org/debian trixie/main amd64 r-cran-r.oo all 1.26.0-1 [961 kB] Get:615 http://deb.debian.org/debian trixie/main amd64 r-cran-r.utils all 2.12.3-1 [1396 kB] Get:616 http://deb.debian.org/debian trixie/main amd64 r-cran-zip amd64 2.3.1-1 [118 kB] Get:617 http://deb.debian.org/debian trixie/main amd64 r-cran-openxlsx amd64 4.2.7.1-1 [2014 kB] Get:618 http://deb.debian.org/debian trixie/main amd64 r-cran-rio all 1.2.3-1 [531 kB] Get:619 http://deb.debian.org/debian trixie/main amd64 r-cran-car all 3.1-3-1 [1533 kB] Get:620 http://deb.debian.org/debian trixie/main amd64 r-cran-rstatix all 0.7.2-1 [609 kB] Get:621 http://deb.debian.org/debian trixie/main amd64 r-cran-ggpubr all 0.6.0-1 [2080 kB] Get:622 http://deb.debian.org/debian trixie/main amd64 r-cran-miniui all 0.1.1.1-3 [35.9 kB] Get:623 http://deb.debian.org/debian trixie/main amd64 r-cran-shinyjs all 2.1.0-1 [1009 kB] Get:624 http://deb.debian.org/debian trixie/main amd64 r-cran-colourpicker all 1.3.0+dfsg-1 [1212 kB] Get:625 http://deb.debian.org/debian trixie/main amd64 r-cran-plotly all 4.10.4+dfsg-2 [3634 kB] Get:626 http://deb.debian.org/debian trixie/main amd64 r-cran-gprofiler2 all 0.2.3+dfsg-1 [121 kB] Get:627 http://deb.debian.org/debian trixie/main amd64 r-cran-pheatmap all 1.0.12-2 [77.9 kB] Get:628 http://deb.debian.org/debian trixie/main amd64 salmon amd64 1.10.2+ds1-1+b4 [3404 kB] Get:629 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get:630 http://deb.debian.org/debian trixie/main amd64 python3-configargparse all 1.7-1 [31.3 kB] Get:631 http://deb.debian.org/debian trixie/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get:632 http://deb.debian.org/debian trixie/main amd64 python3-datrie amd64 0.8.2-5 [124 kB] Get:633 http://deb.debian.org/debian trixie/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get:634 http://deb.debian.org/debian trixie/main amd64 python3-gitdb all 4.0.11-1 [45.5 kB] Get:635 http://deb.debian.org/debian trixie/main amd64 python3-git all 3.1.37-3 [137 kB] Get:636 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get:637 http://deb.debian.org/debian trixie/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get:638 http://deb.debian.org/debian trixie/main amd64 python3-py all 1.11.0-2 [88.7 kB] Get:639 http://deb.debian.org/debian trixie/main amd64 python3-retry all 0.9.2-3 [7088 B] Get:640 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-3 [43.3 kB] Get:641 http://deb.debian.org/debian trixie/main amd64 python3-smart-open all 7.0.4-2 [83.3 kB] Get:642 http://deb.debian.org/debian trixie/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get:643 http://deb.debian.org/debian trixie/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:644 http://deb.debian.org/debian trixie/main amd64 python3-toposort all 1.10-2 [7336 B] Get:645 http://deb.debian.org/debian trixie/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get:646 http://deb.debian.org/debian trixie/main amd64 python3-plac all 1.4.3-1 [65.6 kB] Get:647 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get:648 http://deb.debian.org/debian trixie/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get:649 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-6 [318 kB] Get:650 http://deb.debian.org/debian trixie/main amd64 trim-galore all 0.6.10-1 [17.8 MB] Get:651 http://deb.debian.org/debian trixie/main amd64 pigx-rnaseq all 0.1.1-1 [61.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 587 MB in 57s (10.3 MB/s) Selecting previously unselected package libapparmor1: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 ... 5171 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b2_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b2) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_256.7-3_amd64.deb ... Unpacking libsystemd-shared:amd64 (256.7-3) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_256.7-3_amd64.deb ... Unpacking systemd (256.7-3) ... Setting up libapparmor1:amd64 (3.1.7-1+b2) ... Setting up libsystemd-shared:amd64 (256.7-3) ... Setting up systemd (256.7-3) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. [ESC][0;1;39m/usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring.[ESC][0m [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Selecting previously unselected package systemd-sysv. (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 .../0-systemd-sysv_256.7-3_amd64.deb ... Unpacking systemd-sysv (256.7-3) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.14.10-6_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.10-6) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.14.10-6_amd64.deb ... Unpacking dbus-bin (1.14.10-6) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../3-dbus-session-bus-common_1.14.10-6_all.deb ... Unpacking dbus-session-bus-common (1.14.10-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../4-libexpat1_2.6.3-2_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-2) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../5-dbus-daemon_1.14.10-6_amd64.deb ... Unpacking dbus-daemon (1.14.10-6) ... Selecting previously unselected package adduser. Preparing to unpack .../6-adduser_3.137_all.deb ... Unpacking adduser (3.137) ... Setting up adduser (3.137) ... Selecting previously unselected package dbus-system-bus-common. (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 ... 6265 files and directories currently installed.) Preparing to unpack .../0-dbus-system-bus-common_1.14.10-6_all.deb ... Unpacking dbus-system-bus-common (1.14.10-6) ... Selecting previously unselected package dbus. Preparing to unpack .../1-dbus_1.14.10-6_amd64.deb ... Unpacking dbus (1.14.10-6) ... Selecting previously unselected package perl-modules-5.40. Preparing to unpack .../2-perl-modules-5.40_5.40.0-6_all.deb ... Unpacking perl-modules-5.40 (5.40.0-6) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../3-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../4-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../5-libperl5.40_5.40.0-6_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-6) ... Selecting previously unselected package perl. Preparing to unpack .../6-perl_5.40.0-6_amd64.deb ... Unpacking perl (5.40.0-6) ... Selecting previously unselected package pigz. Preparing to unpack .../7-pigz_2.8-1_amd64.deb ... Unpacking pigz (2.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../8-libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../9-python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-2) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 8778 files and directories currently installed.) 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... 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Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up rpcsvc-proto (1.4.3-1) ... Setting up libasound2t64:amd64 (1.2.12-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-3.2) ... Setting up libapache-pom-java (33-2) ... Setting up libavahi-common-data:amd64 (0.8-13+b3) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up libdbus-1-3:amd64 (1.14.10-6) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libquadmath0:amd64 (14.2.0-6) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libjs-d3 (3.5.17-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up libatomic1:amd64 (14.2.0-6) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:amd64 (2.3.0-2) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libglapi-mesa:amd64 (24.2.4-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-6) ... Setting up libvulkan1:amd64 (1.3.296.0-1) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libubsan1:amd64 (14.2.0-6) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2+b1) ... Setting up libgif7:amd64 (5.2.2-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... Setting up perl-modules-5.40 (5.40.0-6) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b2) ... Setting up libhwasan0:amd64 (14.2.0-6) ... Setting up pigz (2.8-1) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-5) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.14.10-6) ... Setting up libasan8:amd64 (14.2.0-6) ... Setting up procps (2:4.0.4-6) ... Setting up liblua5.4-0:amd64 (5.4.6-3+b2) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up git-man (1:2.45.2-1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b2) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up node-bootstrap-sass (3.4.3-2) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libwayland-egl1:amd64 (1.23.0-1+b1) ... Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libtsan2:amd64 (14.2.0-6) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up dbus-system-bus-common (1.14.10-6) ... Setting up libc-dev-bin (2.40-3) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up node-normalize.css (8.0.1-5) ... Setting up libdrm-common (2.4.123-1) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up dbus-bin (1.14.10-6) ... Setting up liblsan0:amd64 (14.2.0-6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libitm1:amd64 (14.2.0-6) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Setting up libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b2) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.3-1) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-13+b3) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnss3:amd64 (2:3.105-2) ... Setting up dbus-daemon (1.14.10-6) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Setting up libtbbbind-2-5:amd64 (2021.12.0-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.11+ds-1+b1) ... Setting up libperl5.40:amd64 (5.40.0-6) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-6) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ... Setting up libjs-jquery-metadata (12-4) ... Setting up dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ... Setting up xml-core (0.19) ... Setting up libjson-perl (4.10000-1) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libpam-systemd:amd64 (256.7-3) ... Setting up libc6-dev:amd64 (2.40-3) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libgcc-14-dev:amd64 (14.2.0-6) ... Setting up libcommons-codec-java (1.17.1-1) ... Setting up libstdc++-14-dev:amd64 (14.2.0-6) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libavahi-client3:amd64 (0.8-13+b3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (4.16.3+ds-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.2) ... Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.10.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b2) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libxcursor1:amd64 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up python3.12-tk (3.12.6-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up libtbb12:amd64 (2021.12.0-1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.0-1) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up liberror-perl (0.17029-2) ... Setting up libdconf1:amd64 (0.40.0-4+b3) ... Setting up dbus-user-session (1.14.10-6) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up git (1:2.45.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libbigwig0t64:amd64 (0.4.7+dfsg-3.1+b2) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-9) ... Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Setting up mesa-libgallium:amd64 (24.2.4-1) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-9) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libgbm1:amd64 (24.2.4-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.6-1) ... Setting up libgl1-mesa-dri:amd64 (24.2.4-1) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up samtools (1.20-3) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up salmon (1.10.2+ds1-1+b4) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-squarem (2021.1-1) ... Setting up megadepth (1.2.0-4+b1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-formula (1.2-5-1) ... Setting up r-cran-zip (2.3.1-1) ... Setting up r-cran-xml (3.99-0.17-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-locfit (1.5-9.10-1) ... Setting up r-cran-sparsem (1.84-2-1+b1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up r-cran-clipr (0.8.0-1) ... Setting up r-cran-polynom (1.4-1+dfsg-1) ... Setting up r-cran-commonmark (1.9.1-1) ... Setting up r-cran-rjson (0.2.23-1) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-9) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-numderiv (2016.8-1.1-3) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-2) ... Setting up r-bioc-genomeinfodbdata (1.2.12-1) ... Setting up r-cran-microbenchmark (1.5.0-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.4+dfsg-1) ... Setting up r-cran-rcpp (1.0.13-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-nloptr (2.1.1-1) ... Setting up r-cran-boot (1.3-31-1) ... Setting up r-cran-rematch (2.0.0-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up libglx-mesa0:amd64 (24.2.4-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up r-cran-listenv (0.9.1+dfsg-1) ... Setting up littler (0.3.20-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Setting up r-bioc-matrixgenerics (1.16.0-2) ... Setting up r-cran-xfun (0.48+dfsg-1) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-backports (1.5.0-2) ... Setting up r-cran-deriv (4.1.6-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-abind (1.4-8-1) ... Setting up r-cran-digest (0.6.37-1) ... Setting up r-cran-yaml (2.3.10-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-gower (1.0.1-1) ... Setting up r-cran-evaluate (1.0.0-1) ... Setting up r-cran-timedate (4041.110-1) ... Setting up r-cran-highr (0.11+dfsg-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-cardata (3.0.5-1) ... Setting up r-cran-mass (7.3-61-1) ... Setting up python3 (3.12.6-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up python3-zipp (3.20.2-1) ... Setting up r-cran-data.table (1.16.2+dfsg-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-foreign (0.8.87-1) ... Setting up r-cran-writexl (1.5.1-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up python3-markupsafe (2.1.5-1+b1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bitops (1.0-8-1) ... Setting up python3-plac (1.4.3-1) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up python3-tz (2024.1-2) ... Setting up r-cran-progressr (0.14.0-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up r-cran-shape (1.4.6.1-1) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-cran-fastmap (1.2.0-1) ... Setting up python3-six (1.16.0-7) ... Setting up r-cran-r.methodss3 (1.8.2-1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up r-cran-jsonlite (1.8.9+dfsg-1) ... Setting up python3-pil:amd64 (10.4.0-1) ... Setting up r-cran-corrplot (0.94-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up python3-packaging (24.1-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-parallelly (1.38.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up coinor-cbc (2.10.12+ds-1) ... Setting up r-cran-stringi (1.8.4-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up python3-brotli (1.1.0-2+b5) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-diagram (1.6.5-2) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-dpath (2.2.0-1) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-kiwisolver (1.4.7-2) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-wrapt (1.15.0-3) ... Setting up python3-markdown (3.7-1) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up r-cran-later (1.3.2+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-htmltools (0.5.8.1-1) ... Setting up r-cran-tinytex (0.53-1) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up r-bioc-tximport (1.32.0+dfsg-1) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up r-cran-kernsmooth (2.23-24-1) ... Setting up r-cran-knitr (1.48+dfsg-1) ... Setting up python3-rpds-py (0.20.1-1) ... Setting up python3-fastjsonschema (2.20.0-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up hisat2 (2.2.1-5) ... Setting up python3-lxml:amd64 (5.3.0-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-py2bit (0.3.1-3+b1) ... Setting up r-cran-rcpparmadillo (14.0.2-1-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up python3-datrie:amd64 (0.8.2-5) ... Setting up r-cran-tzdb (0.4.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lzstring (1.0.4-3) ... Setting up r-cran-globals (0.16.3-1) ... Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-smmap (6.0.0-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up python3-jupyter-core (5.7.2-4) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up python3-toposort (1.10-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-configargparse (1.7-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up r-cran-minqa (1.2.8-1) ... Setting up python3-attr (23.2.0-2) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up r-cran-class (7.3-22-2) ... Setting up python3-smart-open (7.0.4-2) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up r-cran-openxlsx (4.2.7.1-1) ... Setting up python3-deeptoolsintervals (0.1.9-3+b9) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ ' """ Setting up r-cran-matrixmodels (0.5-3-1) ... Setting up python3-charset-normalizer (3.4.0-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b2) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up python3-tenacity (8.4.2+really8.4.1-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-clock (0.7.1-1) ... Setting up r-cran-proc (1.18.5-1) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-yaml (6.0.2-1) ... Setting up python3-tk:amd64 (3.12.6-1) ... Setting up r-cran-survival (3.7-0-1) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up python3-gitdb (4.0.11-1) ... Setting up r-cran-r.oo (1.26.0-1) ... Setting up python3-click (8.1.7-2) ... Setting up r-cran-future (1.34.0+dfsg-1) ... Setting up r-cran-forcats (1.0.0-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-lme4 (1.1-35.5-1) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up python3-yte (1.5.4-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-cran-future.apply (1.11.2+dfsg-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pyaml-env (1.2.1-2) ... /usr/lib/python3/dist-packages/pyaml_env/parse_config.py:58: SyntaxWarning: invalid escape sequence '\w' type_tag_pattern = re.compile(f'({type_tag}\w+\s)') Setting up r-cran-timechange (0.3.0-1) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up python3-git (3.1.37-3) ... Setting up libgtk-3-0t64:amd64 (3.24.43-4) ... Setting up r-cran-gridextra (2.3-3) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-lava (1.7.3+dfsg-1) ... Setting up r-cran-promises (1.3.0+dfsg-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-e1071 (1.7-16-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-hardhat (1.4.0+dfsg-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up r-cran-progress (1.2.3-1) ... Setting up python3-referencing (0.35.1-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-lubridate (1.9.3+dfsg-1) ... Setting up r-cran-r.utils (2.12.3-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-cran-prodlim (2024.06.25-1) ... Setting up python3-py (1.11.0-2) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up python3-babel (2.14.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up r-cran-ggsignif (0.6.4-1) ... Setting up r-cran-cellranger (1.1.0-3) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-cran-ggsci (3.2.0-1) ... Setting up python3-networkx (3.2.1-4) ... Setting up r-cran-ipred (0.9-15-1) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up r-cran-ggrepel (0.9.5-2) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up python3-retry (0.9.2-3) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up r-cran-recipes (1.1.0+dfsg-1) ... Setting up python3-colormath (3.0.0-4) ... /usr/lib/python3/dist-packages/colormath/chromatic_adaptation.py:85: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying adaptation matrix: %s", adaptation) /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:684: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:788: SyntaxWarning: invalid escape sequence '\s' """ /usr/lib/python3/dist-packages/colormath/color_conversions.py:40: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying RGB conversion matrix: %s->%s", /usr/lib/python3/dist-packages/colormath/color_conversions.py:488: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target RGB space: %s", target_rgb) /usr/lib/python3/dist-packages/colormath/color_conversions.py:490: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target native illuminant: %s", target_illum) /usr/lib/python3/dist-packages/colormath/color_conversions.py:491: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- XYZ color's illuminant: %s", cobj.illuminant) /usr/lib/python3/dist-packages/colormath/color_conversions.py:497: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", /usr/lib/python3/dist-packages/colormath/color_conversions.py:503: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* New values: %.3f, %.3f, %.3f", /usr/lib/python3/dist-packages/colormath/color_objects.py:452: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Original illuminant: %s", self.illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:453: SyntaxWarning: invalid escape sequence '\-' logger.debug(" \- Target illuminant: %s", target_illuminant) /usr/lib/python3/dist-packages/colormath/color_objects.py:459: SyntaxWarning: invalid escape sequence '\*' logger.debug(" \* Applying transformation from %s to %s ", Setting up python3-pybigwig (0.3.23+dfsg-1) ... Setting up python3-stopit (1.1.2-3) ... Setting up python3-contourpy (1.3.0-2) ... Setting up python3-humanize (4.11.0-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up python3-htseq (2.0.5-2+b1) ... /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' _re_attr_empty = re.compile("^\s*$") /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up python3-dnaio (1.2.2-1) ... Setting up r-cran-cowplot (1.1.3+dfsg-1) ... Setting up r-cran-readxl (1.4.3-1) ... Setting up python3-scipy (1.13.1-5) ... Setting up python3-spectra (0.0.11-4) ... Setting up python3-rich (13.7.1-1) ... Setting up r-cran-haven (2.5.4-1) ... Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-cran-caret (6.0-94+dfsg-1) ... Setting up r-cran-shiny (1.9.1+dfsg-1) ... Setting up r-cran-shinyjs (2.1.0-1) ... Setting up r-cran-miniui (0.1.1.1-3) ... Setting up python3-cutadapt (4.7-2+b1) ... Setting up r-cran-broom (1.0.7+dfsg-1) ... Setting up python3-jsonschema (4.19.2-5) ... Setting up r-cran-rmarkdown (2.28+dfsg-1) ... Setting up r-cran-conquer (1.3.3-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up python3-rich-click (1.6.0-1) ... Setting up r-cran-crosstalk (1.2.1+dfsg-1) ... Setting up r-cran-rio (1.2.3-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-cran-quantreg (5.99-1) ... Setting up cutadapt (4.7-2) ... Setting up r-bioc-deseq2 (1.44.0+dfsg-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up r-cran-modelr (0.1.11-1) ... Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... Setting up r-cran-colourpicker (1.3.0+dfsg-1) ... Setting up python3-plotly (5.20.0+dfsg-1) ... Setting up r-cran-doby (4.6.24-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-cran-dt (0.33+dfsg-1) ... Setting up trim-galore (0.6.10-1) ... Setting up r-cran-plotly (4.10.4+dfsg-2) ... Setting up r-cran-pbkrtest (0.5.3-1) ... Setting up r-cran-car (3.1-3-1) ... Setting up r-cran-gprofiler2 (0.2.3+dfsg-1) ... Setting up r-cran-rstatix (0.7.2-1) ... Setting up r-cran-ggpubr (0.6.0-1) ... Setting up python3-fonttools (4.54.1-4) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3) ... Setting up multiqc (1.21+dfsg-2) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for systemd (256.7-3) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ... Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up fastqc (0.12.1+dfsg-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up snakemake (7.32.4-6) ... Setting up python3-sphinx (7.4.7-4) ... Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-deeptools (3.5.5+dfsg-1) ... Setting up pigx-rnaseq (0.1.1-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 2m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 2m0.2s INFO: Running scripts post_install 2m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m0.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m3.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpdmez5w6x to sid 2m3.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 2m3.3s INFO: Running scripts pre_distupgrade 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_exceptions'] 2m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_exceptions'] 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_zz_database-server'] 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 2m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'update'] 2m5.5s 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 [7333 kB] Fetched 17.6 MB in 2s (10.4 MB/s) Reading package lists... 2m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'update'] 2m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-yf', 'dist-upgrade'] 2m22.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libmbedcrypto16 libmbedtls21 libmbedx509-7 The following packages will be upgraded: bsdutils gcc-14-base git git-man gpgv libasan8 libatomic1 libaudit-common libaudit1 libblkid1 libdebconfclient0 libgbm1 libgcc-14-dev libgcc-s1 libgfortran5 libgl1-mesa-dri libglapi-mesa libglx-mesa0 libgomp1 libhwasan0 libitm1 liblsan0 libmount1 libncbi-ngs3 libncbi-vdb3 libngs-java libngs-jni libpam-systemd libpcsclite1 libperl5.40 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libquadmath0 librhino-java libsmartcols1 libstdc++-14-dev libstdc++6 libsystemd-shared libsystemd0 libtsan2 libubsan1 libudev1 libuuid1 libuv1t64 libx11-6 libx11-data libx11-xcb1 linux-libc-dev login mesa-libgallium mount ncbi-vdb-data perl perl-base perl-modules-5.40 python3-attr python3-pkg-resources python3-smart-open python3.12 python3.12-minimal python3.12-tk r-base-core r-bioc-genomicranges r-cran-commonmark r-cran-dplyr r-cran-rcpp r-cran-xfun systemd systemd-sysv tzdata util-linux 72 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After this operation, 3633 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-10 [105 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-7 [4324 kB] Get:3 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-7 [267 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-7 [1675 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-7 [3017 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-10 [35.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-10 [168 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-10 [199 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-10 [139 kB] Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-10 [1217 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-10 [154 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-3 [12.4 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-3 [54.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-10 [81.4 kB] Get:15 http://deb.debian.org/debian sid/main amd64 systemd-sysv amd64 257~rc1-3 [58.9 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpam-systemd amd64 257~rc1-3 [289 kB] Get:17 http://deb.debian.org/debian sid/main amd64 systemd amd64 257~rc1-3 [3592 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libsystemd-shared amd64 257~rc1-3 [2131 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc1-3 [445 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpython3.12t64 amd64 3.12.7-2 [2150 kB] Get:21 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.7-2 [671 kB] Get:22 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.7-2 [2161 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.7-2 [1967 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.7-2 [815 kB] Get:25 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:26 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.45-2 [219 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:32 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Get:35 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc1-3 [146 kB] Get:44 http://deb.debian.org/debian sid/main amd64 git-man all 1:2.45.2-1.1 [2159 kB] Get:45 http://deb.debian.org/debian sid/main amd64 git amd64 1:2.45.2-1.1 [8662 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.2.6-1 [154 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libgbm1 amd64 24.2.6-1 [42.8 kB] Get:48 http://deb.debian.org/debian sid/main amd64 mesa-libgallium amd64 24.2.6-1 [9185 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.2.6-1 [38.0 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.2.6-1 [43.9 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.2-2 [355 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.2-2 [147 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.2-2 [233 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.9+dfsg-7 [112 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.9+dfsg-7 [25.6 kB] Get:59 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7 [157 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB] Get:63 http://deb.debian.org/debian sid/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:65 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.11.6-1 [2449 kB] Get:66 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:67 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:68 http://deb.debian.org/debian sid/main amd64 python3-smart-open all 7.0.5-1 [98.5 kB] Get:69 http://deb.debian.org/debian sid/main amd64 python3.12-tk amd64 3.12.7-2 [112 kB] Get:70 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:71 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.2+dfsg-1 [1843 kB] Get:72 http://deb.debian.org/debian sid/main amd64 r-cran-commonmark amd64 1.9.2-1 [122 kB] Get:73 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-2 [1542 kB] Get:74 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:75 http://deb.debian.org/debian sid/main amd64 r-cran-xfun amd64 0.49+dfsg-1 [546 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 105 MB in 8s (13.5 MB/s) (Reading database ... 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[ESC][0;1;39m/usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring.[ESC][0m [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Setting up libpython3.12t64:amd64 (3.12.7-2) ... Setting up libperl5.40:amd64 (5.40.0-7) ... Setting up perl (5.40.0-7) ... Setting up libmbedx509-7:amd64 (3.6.2-2) ... Setting up r-base-core (4.4.2-1) ... Installing new version of config file /etc/R/Makeconf ... Setting up git (1:2.45.2-1.1) ... Setting up libmbedtls21:amd64 (3.6.2-2) ... Setting up r-cran-dplyr (1.1.4-2) ... Setting up r-cran-commonmark (1.9.2-1) ... Setting up libgcc-14-dev:amd64 (14.2.0-8) ... Setting up libstdc++-14-dev:amd64 (14.2.0-8) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up systemd-sysv (257~rc1-3) ... Setting up libglx-mesa0:amd64 (24.2.6-1) ... Setting up r-cran-xfun (0.49+dfsg-1) ... Setting up r-bioc-genomicranges (1.56.2+dfsg-1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libpam-systemd:amd64 (257~rc1-3) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for dbus (1.14.10-6) ... Processing triggers for shared-mime-info (2.4-5+b1) ... Processing triggers for hicolor-icon-theme (0.18-1) ... 2m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-yf', 'dist-upgrade'] 2m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m22.5s DUMP: a6fc1d88a982bddb9bc0255e931d8ccb - 2m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 2m22.6s DUMP: Package: pigx-rnaseq Version: 0.1.1-1 Installed-Size: 176 Maintainer: Debian Med Packaging Team Architecture: all Depends: fastp, fastqc, hisat2 | rna-star, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3:any, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt, r-cran-ggplot2, r-cran-ggpubr, r-cran-ggrepel, r-cran-gprofiler2, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore Recommends: hisat2, rna-star Description-en: pipeline for checkpointed and distributed RNA-seq analyses This package provides a automated workflow for the automated analysis of RNA-seq experiments. A series of well-accecpted tools are connected in Python scripts and controlled via snakemake. This supports the parallel execution of these workflows and provides checkpointing, such that interrupted workflows can take up their work again. Description-md5: e48b7ff1eb2b189a5bedb2ce0c32035c Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq Section: science Priority: optional Filename: pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.1-1_all.deb Size: 61696 MD5sum: 31284ff2cec66262fab4b45074a1c1ad SHA256: 286ce30816f15c9348617ee7aa74d60a29c39d94b0942b330eee7df942b6192a 2m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 2m22.6s INFO: apt-cache knows about the following packages: pigx-rnaseq 2m22.6s INFO: Running scripts pre_install 2m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 2m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 2m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 2m22.7s 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: 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 2m22.7s DUMP: pigx-rnaseq: Installed: 0.1.1-1 Candidate: 0.1.1-1 Version table: *** 0.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 2m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 2m23.0s DUMP: Reading package lists... Building dependency tree... Reading state information... pigx-rnaseq is already the newest version (0.1.1-1). The following packages were automatically installed and are no longer required: libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 2m23.0s INFO: Running scripts post_install 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m23.0s INFO: Running scripts post_distupgrade 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_exceptions'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_exceptions'] 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_zz_backports'] 2m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_distupgrade_zz_backports'] 2m23.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m26.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m26.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m29.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m29.4s INFO: Running scripts pre_install 2m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_database-server'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_exceptions'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_extras'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 2m29.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 2m29.5s DUMP: pigx-rnaseq: Installed: 0.1.1-1 Candidate: 0.1.1-1 Version table: *** 0.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-cache', 'policy', 'pigx-rnaseq'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 2m29.8s DUMP: Reading package lists... Building dependency tree... Reading state information... pigx-rnaseq is already the newest version (0.1.1-1). The following packages were automatically installed and are no longer required: libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 2m29.8s INFO: Running scripts post_install 2m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_install_exceptions'] 2m29.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m33.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 2m36.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', '-ac', '--ignore-obsolete'] 2m42.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', '-ac', '--ignore-obsolete'] 2m42.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m42.6s DUMP: 0.15.6 2m42.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m42.6s INFO: Running adequate version 0.15.6 now. 2m42.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'pigx-rnaseq'] 2m42.7s DUMP: pigx-rnaseq: py-file-not-bytecompiled /usr/libexec/pigx_rnaseq/scripts/validate_input.py pigx-rnaseq: py-file-not-bytecompiled /usr/libexec/pigx_rnaseq/snakefile.py 2m42.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'pigx-rnaseq'] 2m42.7s ERROR: WARN: Inadequate results from running adequate! pigx-rnaseq: py-file-not-bytecompiled /usr/libexec/pigx_rnaseq/scripts/validate_input.py pigx-rnaseq: py-file-not-bytecompiled /usr/libexec/pigx_rnaseq/snakefile.py 2m42.7s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 2m42.7s INFO: Running scripts pre_remove 2m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m42.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m42.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_exceptions'] 2m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/pre_remove_exceptions'] 2m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m52.4s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 47.0-2 install ok installed apt apt 2.9.10 install ok installed at-spi2-common at-spi2-common 2.54.0-1 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-10 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coinor-cbc coinor-cbc 2.10.12+ds-1 install ok installed coinor-libcbc3.1:amd64 coinor-libcbc3.1 2.10.12+ds-1 install ok installed coinor-libcgl1:amd64 coinor-libcgl1 0.60.9+ds-1 install ok installed coinor-libclp1:amd64 coinor-libclp1 1.17.10+ds-1 install ok installed coinor-libcoinutils3v5:amd64 coinor-libcoinutils3v5 2.11.11+ds-1+b1 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.10+ds-1+b1 install ok installed coreutils coreutils 9.5-1+b1 install ok installed cutadapt cutadapt 4.7-2 install ok installed dash dash 0.5.12-9 install ok installed dbus dbus 1.14.10-6 install ok installed dbus-bin dbus-bin 1.14.10-6 install ok installed dbus-daemon dbus-daemon 1.14.10-6 install ok installed dbus-session-bus-common dbus-session-bus-common 1.14.10-6 install ok installed dbus-system-bus-common dbus-system-bus-common 1.14.10-6 install ok installed dbus-user-session dbus-user-session 1.14.10-6 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-4+b3 install ok installed dconf-service dconf-service 0.40.0-4+b3 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 default-jre default-jre 2:1.21-76 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-1 install ok installed docutils-common docutils-common 0.21.2+dfsg-2 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed fastp fastp 0.23.4+dfsg-1 install ok installed fastqc fastqc 0.12.1+dfsg-4 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1+b1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed git git 1:2.45.2-1.1 install ok installed git-man git-man 1:2.45.2-1.1 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 4.16.3+ds-2 install ok installed gzip gzip 1.12-1.1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-1 install ok installed hisat2 hisat2 2.2.1-5 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed java-common java-common 0.76 install ok installed javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapache-pom-java libapache-pom-java 33-2 install ok installed libapparmor1:amd64 libapparmor1 3.1.7-1+b2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libasan8:amd64 libasan8 14.2.0-8 install ok installed libasound2-data libasound2-data 1.2.12-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.12-1+b1 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.54.0-1 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.54.0-1 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.54.0-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b3 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b3 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b3 install ok installed libbigwig0t64:amd64 libbigwig0t64 0.4.7+dfsg-3.1+b2 install ok installed libblas3:amd64 libblas3 3.12.0-3+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-10 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost-filesystem1.83.0:amd64 libboost-filesystem1.83.0 1.83.0-3.2 install ok installed libboost-iostreams1.83.0:amd64 libboost-iostreams1.83.0 1.83.0-3.2 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-3.2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-3.2 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b5 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 libc-dev-bin libc-dev-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libc6-dev:amd64 libc6-dev 2.40-3 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.2-2 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-1+b1 install ok installed libcolord2:amd64 libcolord2 1.4.7-1+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcommons-codec-java libcommons-codec-java 1.17.1-1 install ok installed libcommons-compress-java libcommons-compress-java 1.27.1-2 install ok installed libcommons-io-java libcommons-io-java 2.17.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-1 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-3 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-2 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.10.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-6 install ok installed libdconf1:amd64 libdconf1 0.40.0-4+b3 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.123-1 install ok installed libdrm-common libdrm-common 2.4.123-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.123-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.123-1 install ok installed libdrm2:amd64 libdrm2 2.4.123-1 install ok installed libedit2:amd64 libedit2 3.1-20240808-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-2 install ok installed liberror-perl liberror-perl 0.17029-2 install ok installed libexpat1:amd64 libexpat1 2.6.3-2 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgbm1:amd64 libgbm1 24.2.6-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-8 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.12+dfsg-1+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-1 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libgif7:amd64 libgif7 5.2.2-1+b1 install ok installed libgl1:amd64 libgl1 1.7.0-1+b2 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.2.6-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.2.6-1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-2 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b2 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.2.6-1 install ok installed libglx0:amd64 libglx0 1.7.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.43-4 install ok installed libgtk-3-common libgtk-3-common 3.24.43-4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libhtsjdk-java libhtsjdk-java 4.1.0+dfsg-2 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-8 install ok installed libhwloc15:amd64 libhwloc15 2.11.2-1 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libisal2 libisal2 2.31.0-0.3 install ok installed libitm1:amd64 libitm1 14.2.0-8 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjbzip2-java libjbzip2-java 0.9.1-8 install ok installed libjemalloc2:amd64 libjemalloc2 5.3.0-2+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-4 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-es5-shim libjs-es5-shim 4.6.7-2 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-jquery-datatables-extensions libjs-jquery-datatables-extensions 0.0+git20150910.28fd64e+dfsg-5 install ok installed libjs-jquery-metadata libjs-jquery-metadata 12-4 install ok installed libjs-jquery-selectize.js libjs-jquery-selectize.js 0.12.6+dfsg-1.1 install ok installed libjs-jquery-tablesorter libjs-jquery-tablesorter 1:2.31.3+dfsg1-4 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-json libjs-json 0~20221030+~1.0.8-1 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libjs-microplugin.js libjs-microplugin.js 0.0.3+dfsg-1.1 install ok installed libjs-modernizr libjs-modernizr 3.13.0-0.1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-6 install ok installed libjs-prettify libjs-prettify 2015.12.04+dfsg-1.1 install ok installed libjs-sifter.js libjs-sifter.js 0.6.0+dfsg-3 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.4.7-4 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libjson-perl libjson-perl 4.10000-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3+b1 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed libllvm19:amd64 libllvm19 1:19.1.3-1 install ok installed liblsan0:amd64 liblsan0 14.2.0-8 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.6-3+b2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-2 install ok installed libmbedcrypto7t64:amd64 libmbedcrypto7t64 2.28.8-1 install ok installed libmbedtls14t64:amd64 libmbedtls14t64 2.28.8-1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-2 install ok installed libmbedx509-1t64:amd64 libmbedx509-1t64 2.28.8-1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmjson-java libmjson-java 1.4.0-3 install ok installed libmount1:amd64 libmount1 2.40.2-10 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.9+dfsg-7 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.9+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.5-2+b1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1+b1 install ok installed libngs-java:amd64 libngs-java 3.0.9+dfsg-7 install ok installed libngs-jni:amd64 libngs-jni 3.0.9+dfsg-7 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnlopt0:amd64 libnlopt0 2.7.1-5+b5 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.105-2 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam-systemd:amd64 libpam-systemd 257~rc1-3 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-3 install ok installed libpaper-utils libpaper-utils 1.1.29+b2 install ok installed libpaper1:amd64 libpaper1 1.1.29+b2 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.0-3 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-7 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-2 install ok installed libpython3.12t64:amd64 libpython3.12t64 3.12.7-2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-8 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librhino-java librhino-java 1.7.15-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 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 libsensors-config libsensors-config 1:3.6.0-10 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-10+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-10 install ok installed libsnappy-java libsnappy-java 1.1.10.5-2 install ok installed libsnappy-jni libsnappy-jni 1.1.10.5-2 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.2.1-1+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstaden-read14t64:amd64 libstaden-read14t64 1.15.0-1.1+b2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd-shared:amd64 libsystemd-shared 257~rc1-3 install ok installed libsystemd0:amd64 libsystemd0 257~rc1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtbb12:amd64 libtbb12 2021.12.0-1 install ok installed libtbbbind-2-5:amd64 libtbbbind-2-5 2021.12.0-1 install ok installed libtbbmalloc2:amd64 libtbbmalloc2 2021.12.0-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-8 install ok installed libubsan1:amd64 libubsan1 14.2.0-8 install ok installed libudev1:amd64 libudev1 257~rc1-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-10 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 install ok installed libvulkan1:amd64 libvulkan1 1.3.296.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.0-1+b1 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.0-1+b1 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.0-1+b1 install ok installed libwayland-server0:amd64 libwayland-server0 1.23.0-1+b1 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.17.0-2+b1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.17.0-2+b1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.17.0-2+b1 install ok installed libxcb-present0:amd64 libxcb-present0 1.17.0-2+b1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.17.0-2+b1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.17.0-2+b1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.6-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.2-1+b1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b2 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.6.0-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1+b2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1+b2 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed linux-libc-dev linux-libc-dev 6.11.6-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-10 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed megadepth megadepth 1.2.0-4+b1 install ok installed mesa-libgallium:amd64 mesa-libgallium 24.2.6-1 install ok installed mount mount 2.40.2-10 install ok installed multiqc multiqc 1.21+dfsg-2 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.9+dfsg-2 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed node-bootstrap-sass node-bootstrap-sass 3.4.3-2 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openjdk-21-jre:amd64 openjdk-21-jre 21.0.5+11-1 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.5+11-1 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed pandoc pandoc 3.1.11.1+ds-2 install ok installed pandoc-data pandoc-data 3.1.11.1-3 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.40.0-7 install ok installed perl-base perl-base 5.40.0-7 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-7 install ok installed pigx-rnaseq pigx-rnaseq 0.1.1-1 install ok installed pigz pigz 2.8-1 install ok installed procps procps 2:4.0.4-6 install ok installed python-babel-localedata python-babel-localedata 2.14.0-1 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.12.6-1 install ok installed python3-alabaster python3-alabaster 0.7.16-0.1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-babel python3-babel 2.14.0-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b5 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1 install ok installed python3-click python3-click 8.1.7-2 install ok installed python3-colorama python3-colorama 0.4.6-4 install ok installed python3-coloredlogs python3-coloredlogs 15.0.1-1 install ok installed python3-colormath python3-colormath 3.0.0-4 install ok installed python3-configargparse python3-configargparse 1.7-1 install ok installed python3-connection-pool python3-connection-pool 0.0.3-2 install ok installed python3-contourpy python3-contourpy 1.3.0-2 install ok installed python3-cutadapt python3-cutadapt 4.7-2+b1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-datrie:amd64 python3-datrie 0.8.2-5 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-deeptools python3-deeptools 3.5.5+dfsg-1 install ok installed python3-deeptoolsintervals python3-deeptoolsintervals 0.1.9-3+b9 install ok installed python3-defusedxml python3-defusedxml 0.7.1-2 install ok installed python3-dnaio python3-dnaio 1.2.2-1 install ok installed python3-docutils python3-docutils 0.21.2+dfsg-2 install ok installed python3-dpath python3-dpath 2.2.0-1 install ok installed python3-fastjsonschema python3-fastjsonschema 2.20.0-1 install ok installed python3-fonttools python3-fonttools 4.54.1-4 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-git python3-git 3.1.37-3 install ok installed python3-gitdb python3-gitdb 4.0.11-1 install ok installed python3-htseq python3-htseq 2.0.5-2+b1 install ok installed python3-humanfriendly python3-humanfriendly 10.0-6 install ok installed python3-humanize python3-humanize 4.11.0-1 install ok installed python3-idna python3-idna 3.8-2 install ok installed python3-imagesize python3-imagesize 1.4.1-1 install ok installed python3-importlib-metadata python3-importlib-metadata 8.5.0-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-jinja2 python3-jinja2 3.1.3-1 install ok installed python3-jsonschema python3-jsonschema 4.19.2-5 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-jupyter-core python3-jupyter-core 5.7.2-4 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-2 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b4 install ok installed python3-lzstring python3-lzstring 1.0.4-3 install ok installed python3-markdown python3-markdown 3.7-1 install ok installed python3-markdown-it python3-markdown-it 3.0.0-2 install ok installed python3-markupsafe python3-markupsafe 2.1.5-1+b1 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3 install ok installed python3-mdurl python3-mdurl 0.1.2-1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-nbformat python3-nbformat 5.9.1-1 install ok installed python3-networkx python3-networkx 3.2.1-4 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-numpydoc python3-numpydoc 1.6.0-2 install ok installed python3-packaging python3-packaging 24.1-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1 install ok installed python3-pkg-resources python3-pkg-resources 75.2.0-1 install ok installed python3-plac python3-plac 1.4.3-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-plotly python3-plotly 5.20.0+dfsg-1 install ok installed python3-psutil python3-psutil 5.9.8-2 install ok installed python3-pulp python3-pulp 2.7.0+dfsg-4 install ok installed python3-py python3-py 1.11.0-2 install ok installed python3-py2bit python3-py2bit 0.3.1-3+b1 install ok installed python3-pyaml-env python3-pyaml-env 1.2.1-2 install ok installed python3-pybigwig python3-pybigwig 0.3.23+dfsg-1 install ok installed python3-pygments python3-pygments 2.18.0+dfsg-1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b1 install ok installed python3-ratelimiter python3-ratelimiter 1.2.0.post0-4 install ok installed python3-referencing python3-referencing 0.35.1-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-retry python3-retry 0.9.2-3 install ok installed python3-rich python3-rich 13.7.1-1 install ok installed python3-rich-click python3-rich-click 1.6.0-1 install ok installed python3-roman python3-roman 4.2-1 install ok installed python3-rpds-py python3-rpds-py 0.20.1-1 install ok installed python3-scipy python3-scipy 1.13.1-5 install ok installed python3-six python3-six 1.16.0-7 install ok installed python3-smart-open python3-smart-open 7.0.5-1 install ok installed python3-smmap python3-smmap 6.0.0-1 install ok installed python3-snowballstemmer python3-snowballstemmer 2.2.0-4 install ok installed python3-spectra python3-spectra 0.0.11-4 install ok installed python3-sphinx python3-sphinx 7.4.7-4 install ok installed python3-stopit python3-stopit 1.1.2-3 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-tenacity python3-tenacity 8.4.2+really8.4.1-1 install ok installed python3-throttler python3-throttler 1.2.2-2 install ok installed python3-tk:amd64 python3-tk 3.12.6-1 install ok installed python3-toposort python3-toposort 1.10-2 install ok installed python3-traitlets python3-traitlets 5.14.3+really5.14.3-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b2 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3-wrapt python3-wrapt 1.15.0-3 install ok installed python3-xopen python3-xopen 1.7.0-2 install ok installed python3-yaml python3-yaml 6.0.2-1 install ok installed python3-yte python3-yte 1.5.4-1 install ok installed python3-zipp python3-zipp 3.20.2-1 install ok installed python3.12 python3.12 3.12.7-2 install ok installed python3.12-minimal python3.12-minimal 3.12.7-2 install ok installed python3.12-tk python3.12-tk 3.12.7-2 install ok installed python3.13-tk python3.13-tk 3.13.0-1 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-bioc-biobase r-bioc-biobase 2.64.0-4 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.14.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.38.0-2 install ok installed r-bioc-biostrings r-bioc-biostrings 2.72.1+dfsg-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.30.1+dfsg-1 install ok installed r-bioc-deseq2 r-bioc-deseq2 1.44.0+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.40.1+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.12-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.40.0-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.56.2+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.38.1-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.16.0-2 install ok installed r-bioc-rhtslib r-bioc-rhtslib 3.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.20.0+dfsg-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.64.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.4.1+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.42.1+dfsg-2 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.4.8+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.34.0+dfsg-1 install ok installed r-bioc-tximport r-bioc-tximport 1.32.0+dfsg-1 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.0.0+ds-2 install ok installed r-bioc-xvector r-bioc-xvector 0.44.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.50.0+dfsg-2 install ok installed r-cran-abind r-cran-abind 1.4-8-1 install ok installed r-cran-askpass r-cran-askpass 1.2.1-1 install ok installed r-cran-backports r-cran-backports 1.5.0-2 install ok installed r-cran-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-8-1 install ok installed r-cran-boot r-cran-boot 1.3-31-1 install ok installed r-cran-broom r-cran-broom 1.0.7+dfsg-1 install ok installed r-cran-bslib r-cran-bslib 0.7.0+dfsg-1 install ok installed r-cran-cachem r-cran-cachem 1.1.0-1 install ok installed r-cran-car r-cran-car 3.1-3-1 install ok installed r-cran-cardata r-cran-cardata 3.0.5-1 install ok installed r-cran-caret r-cran-caret 6.0-94+dfsg-1 install ok installed r-cran-cellranger r-cran-cellranger 1.1.0-3 install ok installed r-cran-class r-cran-class 7.3-22-2 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-clipr r-cran-clipr 0.8.0-1 install ok installed r-cran-clock r-cran-clock 0.7.1-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-1+dfsg-1 install ok installed r-cran-colourpicker r-cran-colourpicker 1.3.0+dfsg-1 install ok installed r-cran-commonmark r-cran-commonmark 1.9.2-1 install ok installed r-cran-conquer r-cran-conquer 1.3.3-1 install ok installed r-cran-corrplot r-cran-corrplot 0.94-1 install ok installed r-cran-cowplot r-cran-cowplot 1.1.3+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.5.0-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-crosstalk r-cran-crosstalk 1.2.1+dfsg-1 install ok installed r-cran-curl r-cran-curl 5.2.3+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.16.2+dfsg-1 install ok installed r-cran-deriv r-cran-deriv 4.1.6-1 install ok installed r-cran-diagram r-cran-diagram 1.6.5-2 install ok installed r-cran-digest r-cran-digest 0.6.37-1 install ok installed r-cran-doby r-cran-doby 4.6.24-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-2 install ok installed r-cran-dt r-cran-dt 0.33+dfsg-1 install ok installed r-cran-e1071 r-cran-e1071 1.7-16-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 1.0.0-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.2-1 install ok installed r-cran-fastmap r-cran-fastmap 1.2.0-1 install ok installed r-cran-fontawesome r-cran-fontawesome 0.5.2-1 install ok installed r-cran-forcats r-cran-forcats 1.0.0-1 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-foreign r-cran-foreign 0.8.87-1 install ok installed r-cran-formatr r-cran-formatr 1.14-2 install ok installed r-cran-formula r-cran-formula 1.2-5-1 install ok installed r-cran-fs r-cran-fs 1.6.4+dfsg-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-future r-cran-future 1.34.0+dfsg-1 install ok installed r-cran-future.apply r-cran-future.apply 1.11.2+dfsg-1 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.5.1+dfsg-1 install ok installed r-cran-ggpubr r-cran-ggpubr 0.6.0-1 install ok installed r-cran-ggrepel r-cran-ggrepel 0.9.5-2 install ok installed r-cran-ggsci r-cran-ggsci 3.2.0-1 install ok installed r-cran-ggsignif r-cran-ggsignif 0.6.4-1 install ok installed r-cran-globals r-cran-globals 0.16.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gower r-cran-gower 1.0.1-1 install ok installed r-cran-gprofiler2 r-cran-gprofiler2 0.2.3+dfsg-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.6+dfsg-1 install ok installed r-cran-hardhat r-cran-hardhat 1.4.0+dfsg-1 install ok installed r-cran-haven r-cran-haven 2.5.4-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-htmltools r-cran-htmltools 0.5.8.1-1 install ok installed r-cran-htmlwidgets r-cran-htmlwidgets 1.6.4+dfsg-1 install ok installed r-cran-httpuv r-cran-httpuv 1.6.15+dfsg-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-ipred r-cran-ipred 0.9-15-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-jquerylib r-cran-jquerylib 0.1.4+dfsg-4 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.9+dfsg-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-24-1 install ok installed r-cran-knitr r-cran-knitr 1.48+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-later r-cran-later 1.3.2+dfsg-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lava r-cran-lava 1.7.3+dfsg-1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.2-1+b1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-listenv r-cran-listenv 0.9.1+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-lme4 r-cran-lme4 1.1-35.5-1 install ok installed r-cran-locfit r-cran-locfit 1.5-9.10-1 install ok installed r-cran-lubridate r-cran-lubridate 1.9.3+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-61-1 install ok installed r-cran-matrix r-cran-matrix 1.7-1-1 install ok installed r-cran-matrixmodels r-cran-matrixmodels 0.5-3-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.4.1-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-microbenchmark r-cran-microbenchmark 1.5.0-1 install ok installed r-cran-mime r-cran-mime 0.12-2 install ok installed r-cran-miniui r-cran-miniui 0.1.1.1-3 install ok installed r-cran-minqa r-cran-minqa 1.2.8-1 install ok installed r-cran-modelmetrics r-cran-modelmetrics 1.2.2.2-1+b1 install ok installed r-cran-modelr r-cran-modelr 0.1.11-1 install ok installed r-cran-munsell r-cran-munsell 0.5.1-1 install ok installed r-cran-nlme r-cran-nlme 3.1.166-1 install ok installed r-cran-nloptr r-cran-nloptr 2.1.1-1 install ok installed r-cran-nnet r-cran-nnet 7.3-19-2 install ok installed r-cran-numderiv r-cran-numderiv 2016.8-1.1-3 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-openxlsx r-cran-openxlsx 4.2.7.1-1 install ok installed r-cran-parallelly r-cran-parallelly 1.38.0-1 install ok installed r-cran-pbkrtest r-cran-pbkrtest 0.5.3-1 install ok installed r-cran-pheatmap r-cran-pheatmap 1.0.12-2 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.4-1 install ok installed r-cran-plotly r-cran-plotly 4.10.4+dfsg-2 install ok installed r-cran-plyr r-cran-plyr 1.8.9-1 install ok installed r-cran-polynom r-cran-polynom 1.4-1+dfsg-1 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-proc r-cran-proc 1.18.5-1 install ok installed r-cran-prodlim r-cran-prodlim 2024.06.25-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-progressr r-cran-progressr 0.14.0-1 install ok installed r-cran-promises r-cran-promises 1.3.0+dfsg-1 install ok installed r-cran-proxy r-cran-proxy 0.4-27-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-quantreg r-cran-quantreg 5.99-1 install ok installed r-cran-r.methodss3 r-cran-r.methodss3 1.8.2-1 install ok installed r-cran-r.oo r-cran-r.oo 1.26.0-1 install ok installed r-cran-r.utils r-cran-r.utils 2.12.3-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.13-1-1 install ok installed r-cran-rcpparmadillo r-cran-rcpparmadillo 14.0.2-1-1 install ok installed r-cran-rcppeigen r-cran-rcppeigen 0.3.4.0.2-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.16+dfsg-1 install ok installed r-cran-readr r-cran-readr 2.1.5-1 install ok installed r-cran-readxl r-cran-readxl 1.4.3-1 install ok installed r-cran-recipes r-cran-recipes 1.1.0+dfsg-1 install ok installed r-cran-rematch r-cran-rematch 2.0.0-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.4-2 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rio r-cran-rio 1.2.3-1 install ok installed r-cran-rjson r-cran-rjson 0.2.23-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.28+dfsg-1 install ok installed r-cran-rpart r-cran-rpart 4.1.23-1 install ok installed r-cran-rstatix r-cran-rstatix 0.7.2-1 install ok installed r-cran-sass r-cran-sass 0.4.9+dfsg-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-shape r-cran-shape 1.4.6.1-1 install ok installed r-cran-shiny r-cran-shiny 1.9.1+dfsg-1 install ok installed r-cran-shinyjs r-cran-shinyjs 2.1.0-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-sourcetools r-cran-sourcetools 0.1.7-1-1 install ok installed r-cran-sparsem r-cran-sparsem 1.84-2-1+b1 install ok installed r-cran-squarem r-cran-squarem 2021.1-1 install ok installed r-cran-statmod r-cran-statmod 1.5.0-1 install ok installed r-cran-stringi r-cran-stringi 1.8.4-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-survival r-cran-survival 3.7-0-1 install ok installed r-cran-sys r-cran-sys 3.4.3-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-timechange r-cran-timechange 0.3.0-1 install ok installed r-cran-timedate r-cran-timedate 4041.110-1 install ok installed r-cran-tinytex r-cran-tinytex 0.53-1 install ok installed r-cran-tzdb r-cran-tzdb 0.4.0-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-vroom r-cran-vroom 1.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.2+dfsg-1 install ok installed r-cran-writexl r-cran-writexl 1.5.1-1 install ok installed r-cran-xfun r-cran-xfun 0.49+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.17-1 install ok installed r-cran-xtable r-cran-xtable 1:1.8-4-2 install ok installed r-cran-yaml r-cran-yaml 2.3.10-1 install ok installed r-cran-zip r-cran-zip 2.3.1-1 install ok installed readline-common readline-common 8.2-5 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed salmon salmon 1.10.2+ds1-1+b4 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sgml-base sgml-base 1.31 install ok installed shared-mime-info shared-mime-info 2.4-5+b1 install ok installed snakemake snakemake 7.32.4-6 install ok installed sphinx-common sphinx-common 7.4.7-4 install ok installed systemd systemd 257~rc1-3 install ok installed systemd-sysv systemd-sysv 257~rc1-3 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed trim-galore trim-galore 0.6.10-1 install ok installed tzdata tzdata 2024b-3 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-10 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xkb-data xkb-data 2.42-1 install ok installed xml-core xml-core 0.19 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1 2m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cutadapt', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libapache-pom-java', 'libapparmor1:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0t64:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libmjson-java', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'megadepth', 'mesa-libgallium:amd64', 'multiqc', 'ncbi-vdb-data', 'netbase', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'pigz', 'procps', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-defusedxml', 'python3-dnaio', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-humanize', 'python3-idna', 'python3-imagesize', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-plotly', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pyaml-env', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pysam', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yte', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-backports', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-boot', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-car', 'r-cran-cardata', 'r-cran-caret', 'r-cran-cellranger', 'r-cran-class', 'r-cran-cli', 'r-cran-clipr', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-colourpicker', 'r-cran-commonmark', 'r-cran-conquer', 'r-cran-corrplot', 'r-cran-cowplot', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-data.table', 'r-cran-deriv', 'r-cran-diagram', 'r-cran-digest', 'r-cran-doby', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-e1071', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-forcats', 'r-cran-foreach', 'r-cran-foreign', 'r-cran-formatr', 'r-cran-formula', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-ggpubr', 'r-cran-ggrepel', 'r-cran-ggsci', 'r-cran-ggsignif', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gprofiler2', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-haven', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lme4', 'r-cran-locfit', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-microbenchmark', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', 'r-cran-modelr', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nloptr', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-openssl', 'r-cran-openxlsx', 'r-cran-parallelly', 'r-cran-pbkrtest', 'r-cran-pheatmap', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-polynom', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shape', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tinytex', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-writexl', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 3m4.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser adwaita-icon-theme at-spi2-common blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cutadapt dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libapache-pom-java libapparmor1 libasan8 libasound2-data libasound2t64 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0t64 libblas3 libboost-dev libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcloudproviders0 libcolord2 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu72 libimagequant0 libisal2 libitm1 libjbig0 libjbzip2-java libjemalloc2 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-metadata libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto16 libmbedcrypto7t64 libmbedtls14t64 libmbedtls21 libmbedx509-1t64 libmbedx509-7 libmjson-java libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnsl2 libnspr4 libnss3 libnuma1 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsqlite3-0 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev littler media-types megadepth mesa-libgallium multiqc ncbi-vdb-data netbase node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre openjdk-21-jre-headless openssl pandoc pandoc-data perl perl-modules-5.40 pigx-rnaseq pigz procps python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-appdirs python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-defusedxml python3-dnaio python3-docutils python3-dpath python3-fastjsonschema python3-fonttools python3-fs python3-git python3-gitdb python3-htseq python3-humanfriendly python3-humanize python3-idna python3-imagesize python3-importlib-metadata python3-inflect python3-jaraco.context python3-jaraco.functools python3-jinja2 python3-jsonschema python3-jsonschema-specifications python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-matplotlib python3-mdurl python3-minimal python3-more-itertools python3-mpmath python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-plac python3-platformdirs python3-plotly python3-psutil python3-pulp python3-py python3-py2bit python3-pyaml-env python3-pybigwig python3-pygments python3-pyparsing python3-pysam python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-traitlets python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yte python3-zipp python3.12 python3.12-minimal python3.12-tk python3.13-tk r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tximport r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-backports r-cran-base64enc r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-boot r-cran-broom r-cran-bslib r-cran-cachem r-cran-car r-cran-cardata r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr r-cran-clock r-cran-codetools r-cran-colorspace r-cran-colourpicker r-cran-commonmark r-cran-conquer r-cran-corrplot r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-data.table r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby r-cran-dplyr r-cran-dt r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-fontawesome r-cran-forcats r-cran-foreach r-cran-foreign r-cran-formatr r-cran-formula r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-ggpubr r-cran-ggrepel r-cran-ggsci r-cran-ggsignif r-cran-globals r-cran-glue r-cran-gower r-cran-gprofiler2 r-cran-gridextra r-cran-gtable r-cran-hardhat r-cran-haven r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lava r-cran-lazyeval r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lme4 r-cran-locfit r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-openssl r-cran-openxlsx r-cran-parallelly r-cran-pbkrtest r-cran-pheatmap r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plotly r-cran-plyr r-cran-polynom r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rstatix r-cran-sass r-cran-scales r-cran-shape r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate r-cran-tinytex r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev 0 upgraded, 0 newly installed, 654 to remove and 0 not upgraded. After this operation, 2209 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 ... 95135 files and directories currently installed.) Removing pigx-rnaseq (0.1.1-1) ... Removing fastqc (0.12.1+dfsg-4) ... Removing default-jre (2:1.21-76) ... Removing openjdk-21-jre:amd64 (21.0.5+11-1) ... Removing libgtk-3-0t64:amd64 (3.24.43-4) ... Removing libgtk-3-common (3.24.43-4) ... Removing dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Removing dconf-service (0.40.0-4+b3) ... Removing dbus-user-session (1.14.10-6) ... Removing libpam-systemd:amd64 (257~rc1-3) ... Removing dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-system-bus-common (1.14.10-6) ... Removing adduser (3.137) ... Removing adwaita-icon-theme (47.0-2) ... Removing libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Removing libatk1.0-0t64:amd64 (2.54.0-1) ... Removing at-spi2-common (2.54.0-1) ... Removing multiqc (1.21+dfsg-2) ... Removing python3-deeptools (3.5.5+dfsg-1) ... Removing python3-matplotlib (3.8.3-3) ... Removing python3-pil.imagetk:amd64 (10.4.0-1) ... Removing python3-pil:amd64 (10.4.0-1) ... Removing python3-tk:amd64 (3.12.6-1) ... Removing blt (2.5.3+dfsg-7) ... Removing snakemake (7.32.4-6) ... Removing python3-numpydoc (1.6.0-2) ... Removing python3-sphinx (7.4.7-4) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... Removing ca-certificates-java (20240118) ... Removing python3-pulp (2.7.0+dfsg-4) ... Removing coinor-cbc (2.10.12+ds-1) ... Removing coinor-libcbc3.1:amd64 (2.10.12+ds-1) ... Removing coinor-libcgl1:amd64 (0.60.9+ds-1) ... Removing coinor-libclp1:amd64 (1.17.10+ds-1) ... Removing coinor-libosi1v5:amd64 (0.108.10+ds-1+b1) ... Removing coinor-libcoinutils3v5:amd64 (2.11.11+ds-1+b1) ... Removing trim-galore (0.6.10-1) ... Removing cutadapt (4.7-2) ... Removing dbus-daemon (1.14.10-6) ... Removing dbus-bin (1.14.10-6) ... Removing dbus-session-bus-common (1.14.10-6) ... Removing python3-docutils (0.21.2+dfsg-2) ... Removing docutils-common (0.21.2+dfsg-2) ... Removing fastp (0.23.4+dfsg-1) ... Removing r-cran-ggpubr (0.6.0-1) ... Removing r-cran-rstatix (0.7.2-1) ... Removing r-cran-car (3.1-3-1) ... Removing r-cran-quantreg (5.99-1) ... Removing r-cran-conquer (1.3.3-1) ... Removing r-cran-caret (6.0-94+dfsg-1) ... Removing r-cran-recipes (1.1.0+dfsg-1) ... Removing r-cran-ipred (0.9-15-1) ... Removing r-cran-rpart (4.1.23-1) ... Removing r-cran-prodlim (2024.06.25-1) ... Removing r-cran-pbkrtest (0.5.3-1) ... Removing r-cran-lme4 (1.1-35.5-1) ... Removing r-cran-rcppeigen (0.3.4.0.2-1) ... Removing r-bioc-rtracklayer (1.64.0-1) ... Removing r-bioc-genomicalignments (1.40.0-1) ... Removing r-bioc-deseq2 (1.44.0+dfsg-1) ... Removing r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Removing r-bioc-delayedarray (0.30.1+dfsg-1) ... Removing r-bioc-sparsearray (1.4.8+dfsg-1) ... Removing r-bioc-s4arrays (1.4.1+dfsg-1) ... Removing r-cran-abind (1.4-8-1) ... Removing r-bioc-rsamtools (2.20.0+dfsg-1) ... Removing r-bioc-biocparallel (1.38.0-2) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-reshape2 (1.4.4-2) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.0-1) ... Removing libcairo-gobject2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing r-cran-gprofiler2 (0.2.3+dfsg-1) ... Removing r-cran-plotly (4.10.4+dfsg-2) ... Removing r-cran-colourpicker (1.3.0+dfsg-1) ... Removing r-cran-shinyjs (2.1.0-1) ... Removing r-cran-dt (0.33+dfsg-1) ... Removing r-cran-htmlwidgets (1.6.4+dfsg-1) ... Removing r-cran-rmarkdown (2.28+dfsg-1) ... Removing r-cran-knitr (1.48+dfsg-1) ... Removing r-cran-crosstalk (1.2.1+dfsg-1) ... Removing fonts-lyx (2.4.2.1-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing python3-git (3.1.37-3) ... Removing git (1:2.45.2-1.1) ... Removing git-man (1:2.45.2-1.1) ... Removing gtk-update-icon-cache (4.16.3+ds-2) ... Removing hicolor-icon-theme (0.18-1) ... Removing hisat2 (2.2.1-5) ... Removing java-common (0.76) ... Removing libhtsjdk-java (4.1.0+dfsg-2) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libcommons-logging-java (1.3.0-1) ... Removing libcommons-compress-java (1.27.1-2) ... Removing systemd-sysv (257~rc1-3) ... Removing systemd (257~rc1-3) ... Removing libapparmor1:amd64 (3.1.7-1+b2) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-3.2) ... Removing libstdc++-14-dev:amd64 (14.2.0-8) ... Removing libgcc-14-dev:amd64 (14.2.0-8) ... Removing libasan8:amd64 (14.2.0-8) ... Removing libasound2t64:amd64 (1.2.12-1+b1) ... Removing libasound2-data (1.2.12-1) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Removing shared-mime-info (2.4-5+b1) ... Removing libcloudproviders0:amd64 (0.3.6-1+b1) ... Removing libatspi2.0-0t64:amd64 (2.54.0-1) ... Removing libcups2t64:amd64 (2.4.10-2) ... Removing libavahi-client3:amd64 (0.8-13+b3) ... Removing libavahi-common3:amd64 (0.8-13+b3) ... Removing libavahi-common-data:amd64 (0.8-13+b3) ... Removing python3-pybigwig (0.3.23+dfsg-1) ... Removing megadepth (1.2.0-4+b1) ... Removing libbigwig0t64:amd64 (0.4.7+dfsg-3.1+b2) ... Removing r-cran-rcpparmadillo (14.0.2-1-1) ... Removing python3-spectra (0.0.11-4) ... Removing python3-colormath (3.0.0-4) ... Removing python3-htseq (2.0.5-2+b1) ... Removing r-cran-ggsignif (0.6.4-1) ... Removing salmon (1.10.2+ds1-1+b4) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-3.2) ... Removing libboost-iostreams1.83.0:amd64 (1.83.0-3.2) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-3.2) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing r-cran-rio (1.2.3-1) ... Removing r-bioc-genomicranges (1.56.2+dfsg-1) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing r-bioc-xvector (0.44.0-1) ... Removing r-bioc-rhtslib (3.0.0+dfsg-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libc6-dev:amd64 (2.40-3) ... Removing libc-dev-bin (2.40-3) ... Removing libcolord2:amd64 (1.4.7-1+b2) ... Removing libcommons-codec-java (1.17.1-1) ... Removing libcommons-io-java (2.17.0-1) ... Removing libcommons-math3-java (3.6.1-3) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Removing samtools (1.20-3) ... Removing python3-datrie:amd64 (0.8.2-5) ... Removing libdbus-1-3:amd64 (1.14.10-6) ... Removing libdconf1:amd64 (0.40.0-4+b3) ... Removing libgl1:amd64 (1.7.0-1+b2) ... Removing libglx0:amd64 (1.7.0-1+b2) ... Removing libglx-mesa0:amd64 (24.2.6-1) ... Removing libgl1-mesa-dri:amd64 (24.2.6-1) ... Removing libgbm1:amd64 (24.2.6-1) ... Removing mesa-libgallium:amd64 (24.2.6-1) ... Removing libdrm-amdgpu1:amd64 (2.4.123-1) ... Removing libdrm-radeon1:amd64 (2.4.123-1) ... Removing libdrm-intel1:amd64 (2.4.123-1) ... Removing libllvm19:amd64 (1:19.1.3-1) ... Removing libedit2:amd64 (3.1-20240808-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libepoxy0:amd64 (1.5.10-2) ... Removing liberror-perl (0.17029-2) ... Removing python3-plotly (5.20.0+dfsg-1) ... Removing python3-nbformat (5.9.1-1) ... Removing python3-jsonschema (4.19.2-5) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.35.1-1) ... Removing python3-rpds-py (0.20.1-1) ... Removing python3-yte (1.5.4-1) ... Removing python3-cutadapt (4.7-2+b1) ... Removing python3-dnaio (1.2.2-1) ... Removing python3-xopen (1.7.0-2) ... Removing python3-stopit (1.1.2-3) ... Removing python3-coloredlogs (15.0.1-1) ... Removing python3-humanfriendly (10.0-6) ... Removing python3-pyaml-env (1.2.1-2) ... Removing python3-yaml (6.0.2-1) ... Removing python3-jupyter-core (5.7.2-4) ... Removing python3-traitlets (5.14.3+really5.14.3-1) ... Removing python3-rich-click (1.6.0-1) ... Removing python3-rich (13.7.1-1) ... Removing python3-deeptoolsintervals (0.1.9-3+b9) ... Removing libpython3.12t64:amd64 (3.12.7-2) ... Removing libfindbin-libs-perl (3.0.2-1) ... Removing sphinx-common (7.4.7-4) ... Removing libjson-perl (4.10000-1) ... Removing perl (5.40.0-7) ... Removing libperl5.40:amd64 (5.40.0-7) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Removing libgif7:amd64 (5.2.2-1+b1) ... Removing libglapi-mesa:amd64 (24.2.6-1) ... Removing libglvnd0:amd64 (1.7.0-1+b2) ... Removing r-cran-gower (1.0.1-1) ... Removing r-cran-modelmetrics (1.2.2.2-1+b1) ... Removing r-cran-data.table (1.16.2+dfsg-1) ... Removing libhwasan0:amd64 (14.2.0-8) ... Removing libtbb12:amd64 (2021.12.0-1) ... Removing libtbbbind-2-5:amd64 (2021.12.0-1) ... Removing libhwloc15:amd64 (2.11.2-1) ... Removing r-cran-doby (4.6.24-1) ... Removing r-cran-modelr (0.1.11-1) ... Removing r-cran-broom (1.0.7+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-openxlsx (4.2.7.1-1) ... Removing r-cran-stringi (1.8.4-1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libisal2 (2.31.0-0.3) ... Removing libitm1:amd64 (14.2.0-8) ... Removing libjbzip2-java (0.9.1-8) ... Removing libjemalloc2:amd64 (5.3.0-2+b2) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-sphinxdoc (7.4.7-4) ... Removing libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... Removing libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Removing libjs-jquery-metadata (12-4) ... Removing libjs-modernizr (3.13.0-0.1) ... Removing libjs-prettify (2015.12.04+dfsg-1.1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblsan0:amd64 (14.2.0-8) ... Removing pandoc (3.1.11.1+ds-2) ... Removing liblua5.4-0:amd64 (5.4.6-3+b2) ... Removing libngs-java:amd64 (3.0.9+dfsg-7) ... Removing libngs-jni:amd64 (3.0.9+dfsg-7) ... Removing libncbi-ngs3:amd64 (3.0.9+dfsg-7) ... Removing libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.2-2) ... Removing libmbedx509-7:amd64 (3.6.2-2) ... Removing libmbedcrypto16:amd64 (3.6.2-2) ... Removing libmbedtls14t64:amd64 (2.28.8-1) ... Removing libmbedx509-1t64:amd64 (2.28.8-1) ... Removing libmbedcrypto7t64:amd64 (2.28.8-1) ... Removing libmjson-java (1.4.0-3) ... Removing libncurses6:amd64 (6.5-2+b1) ... Removing procps (2:4.0.4-6) ... Removing r-cran-nloptr (2.1.1-1) ... Removing libnlopt0:amd64 (2.7.1-5+b5) ... Removing libnss3:amd64 (2:3.105-2) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libpciaccess0:amd64 (0.17-3+b2) ... Removing libpcsclite1:amd64 (2.3.0-3) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libquadmath0:amd64 (14.2.0-8) ... Removing librhino-java (1.7.15-1) ... Removing libsensors5:amd64 (1:3.6.0-10+b1) ... Removing libsensors-config (1:3.6.0-10) ... Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing libsnappy-java (1.1.10.5-2) ... 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Removing libxcb-randr0:amd64 (1.17.0-2+b1) ... Removing libxcomposite1:amd64 (1:0.4.6-1) ... Removing libxcursor1:amd64 (1:1.2.2-1+b1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b2) ... Removing libxfixes3:amd64 (1:6.0.0-2+b2) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b2) ... Removing libxkbcommon0:amd64 (1.6.0-1+b2) ... Removing libxrandr2:amd64 (2:1.5.4-1+b1) ... Removing libxshmfence1:amd64 (1.3-1+b2) ... Removing libyaml-0-2:amd64 (0.2.5-1+b2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing linux-libc-dev (6.11.6-1) ... Removing littler (0.3.20-1) ... Removing ncbi-vdb-data (3.0.9+dfsg-2) ... Removing pandoc-data (3.1.11.1-3) ... Removing perl-modules-5.40 (5.40.0-7) ... Removing pigz (2.8-1) ... Removing python3-babel (2.14.0-1) ... Removing python-babel-localedata (2.14.0-1) ... Removing python3-alabaster (0.7.16-0.1) ... Removing python3-click (8.1.7-2) ... Removing python3-colorama (0.4.6-4) ... Removing python3-configargparse (1.7-1) ... Removing python3-connection-pool (0.0.3-2) ... Removing python3-contourpy (1.3.0-2) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-retry (0.9.2-3) ... Removing python3-defusedxml (0.7.1-2) ... Removing python3-dpath (2.2.0-1) ... Removing python3-fastjsonschema (2.20.0-1) ... Removing python3-gitdb (4.0.11-1) ... Removing python3-humanize (4.11.0-1) ... Removing python3-imagesize (1.4.1-1) ... Removing python3-markdown (3.7-1) ... Removing python3-importlib-metadata (8.5.0-1) ... Removing python3-jinja2 (3.1.3-1) ... Removing python3-kiwisolver (1.4.7-2) ... Removing python3-lzstring (1.0.4-3) ... Removing python3-markdown-it (3.0.0-2) ... Removing python3-markupsafe (2.1.5-1+b1) ... Removing python3-mdurl (0.1.2-1) ... Removing python3-networkx (3.2.1-4) ... Removing python3-packaging (24.1-1) ... Removing python3-plac (1.4.3-1) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-psutil (5.9.8-2) ... Removing python3-py (1.11.0-2) ... Removing python3-py2bit (0.3.1-3+b1) ... Removing python3-pygments (2.18.0+dfsg-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-pysam (0.22.1+ds-2+b1) ... Removing python3-ratelimiter (1.2.0.post0-4) ... Removing python3-roman (4.2-1) ... Removing python3-smart-open (7.0.5-1) ... Removing python3-smmap (6.0.0-1) ... Removing python3-snowballstemmer (2.2.0-4) ... Removing python3-tabulate (0.9.0-1) ... Removing python3-tenacity (8.4.2+really8.4.1-1) ... Removing python3-throttler (1.2.2-2) ... Removing python3-toposort (1.10-2) ... Removing python3-wrapt (1.15.0-3) ... Removing python3-zipp (3.20.2-1) ... Removing r-bioc-biobase (2.64.0-4) ... Removing r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Removing r-bioc-ucsc.utils (1.0.0+ds-2) ... Removing r-bioc-iranges (2.38.1-1) ... Removing r-bioc-tximport (1.32.0+dfsg-1) ... Removing r-bioc-biocio (1.14.0+dfsg-1) ... Removing r-bioc-genomeinfodbdata (1.2.12-1) ... Removing r-bioc-matrixgenerics (1.16.0-2) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... Removing r-cran-askpass (1.2.1-1) ... Removing r-cran-backports (1.5.0-2) ... Removing r-cran-miniui (0.1.1.1-3) ... Removing r-cran-haven (2.5.4-1) ... Removing r-cran-readr (2.1.5-1) ... Removing r-cran-vroom (1.6.5-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-rcurl (1.98-1.16+dfsg-1) ... Removing r-cran-bitops (1.0-8-1) ... Removing r-cran-boot (1.3-31-1) ... Removing r-cran-cardata (3.0.5-1) ... Removing r-cran-readxl (1.4.3-1) ... Removing r-cran-cellranger (1.1.0-3) ... Removing r-cran-e1071 (1.7-16-1) ... Removing r-cran-class (7.3-22-2) ... Removing r-cran-dplyr (1.1.4-2) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-hardhat (1.4.0+dfsg-1) ... Removing r-cran-pheatmap (1.0.12-2) ... Removing r-cran-clipr (0.8.0-1) ... Removing r-cran-clock (0.7.1-1) ... Removing r-cran-lava (1.7.3+dfsg-1) ... Removing r-cran-future.apply (1.11.2+dfsg-1) ... Removing r-cran-future (1.34.0+dfsg-1) ... Removing r-cran-globals (0.16.3-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-corrplot (0.94-1) ... Removing r-cran-cowplot (1.1.3+dfsg-1) ... Removing r-cran-tzdb (0.4.0-2) ... Removing r-cran-lubridate (1.9.3+dfsg-1) ... Removing r-cran-timechange (0.3.0-1) ... Removing r-cran-cpp11 (0.5.0-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-deriv (4.1.6-1) ... Removing r-cran-diagram (1.6.5-2) ... Removing r-cran-progressr (0.14.0-1) ... Removing r-cran-forcats (1.0.0-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (1.0.0-1) ... Removing r-cran-foreign (0.8.87-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-2) ... Removing r-cran-formula (1.2-5-1) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-ggrepel (0.9.5-2) ... Removing r-cran-ggsci (3.2.0-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-kernsmooth (2.23-24-1) ... Removing r-cran-locfit (1.5-9.10-1) ... Removing r-cran-lazyeval (0.2.2-1+b1) ... Removing r-cran-listenv (0.9.1+dfsg-1) ... Removing r-cran-matrixmodels (0.5-3-1) ... Removing r-cran-matrixstats (1.4.1-1) ... Removing r-cran-microbenchmark (1.5.0-1) ... Removing r-cran-minqa (1.2.8-1) ... Removing r-cran-nnet (7.3-19-2) ... Removing r-cran-numderiv (2016.8-1.1-3) ... Removing r-cran-parallelly (1.38.0-1) ... Removing r-cran-proc (1.18.5-1) ... Removing r-cran-plyr (1.8.9-1) ... Removing r-cran-polynom (1.4-1+dfsg-1) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-proxy (0.4-27-1) ... Removing r-cran-r.utils (2.12.3-1) ... Removing r-cran-r.oo (1.26.0-1) ... Removing r-cran-r.methodss3 (1.8.2-1) ... Removing r-cran-rematch (2.0.0-1) ... Removing r-cran-rjson (0.2.23-1) ... Removing r-cran-shape (1.4.6.1-1) ... Removing r-cran-sparsem (1.84-2-1+b1) ... Removing r-cran-squarem (2021.1-1) ... Removing r-cran-statmod (1.5.0-1) ... Removing r-cran-sys (3.4.3-1) ... Removing r-cran-timedate (4041.110-1) ... Removing r-cran-tinytex (0.53-1) ... Removing r-cran-writexl (1.5.1-1) ... Removing r-cran-xfun (0.49+dfsg-1) ... Removing r-cran-yaml (2.3.10-1) ... Removing r-cran-zip (2.3.1-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xkb-data (2.42-1) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing r-cran-survival (3.7-0-1) ... Removing r-cran-shiny (1.9.1+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-bslib (0.7.0+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (11+nmu1) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (33-2) ... Removing r-cran-ggplot2 (3.5.1+dfsg-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-curl (5.2.3+dfsg-1) ... Removing libhts3t64:amd64 (1.20+ds-2) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-2) ... Removing libdrm2:amd64 (2.4.123-1) ... Removing libdrm-common (2.4.123-1) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libjs-d3 (3.5.17-4) ... Removing libjs-es5-shim (4.6.7-2) ... Removing libjs-highlight.js (9.18.5+dfsg1-2) ... Removing r-cran-jquerylib (0.1.4+dfsg-4) ... Removing libjs-jquery-datatables (1.11.5+dfsg-2) ... Removing libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-json (0~20221030+~1.0.8-1) ... Removing libjs-microplugin.js (0.0.3+dfsg-1.1) ... Removing libjs-sifter.js (0.6.0+dfsg-3) ... Removing libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Removing libnghttp3-9:amd64 (1.4.0-1+b1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing r-cran-httpuv (1.6.15+dfsg-1) ... Removing r-cran-sass (0.4.9+dfsg-1) ... Removing r-cran-fs (1.6.4+dfsg-1) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing node-bootstrap-sass (3.4.3-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.4.0-1) ... Removing python3-idna (3.8-2) ... Removing python3-urllib3 (2.0.7-2) ... Removing r-bioc-s4vectors (0.42.1+dfsg-2) ... Removing r-bioc-biocgenerics (0.50.0-2) ... Removing r-cran-fontawesome (0.5.2-1) ... Removing r-cran-htmltools (0.5.8.1-1) ... Removing r-cran-base64enc (0.1-3-3) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.1.0-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-munsell (0.5.1-1) ... Removing r-cran-colorspace (2.1-1+dfsg-1) ... Removing r-cran-commonmark (1.9.2-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-digest (0.6.37-1) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-promises (1.3.0+dfsg-1) ... Removing r-cran-fastmap (1.2.0-1) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.9+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-later (1.3.2+dfsg-1) ... Removing r-cran-nlme (3.1.166-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-61-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-sourcetools (0.1.7-1-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-cran-rcpp (1.0.13-1-1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-cli (3.6.3-1) ... Removing r-base-core (4.4.2-1) ... Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-3) ... Removing fontconfig (2.15.0-1.1+b1) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.10.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b5) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpaper-utils (1.1.29+b2) ... Removing libpaper1:amd64 (1.1.29+b2) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libthai-data (0.1.29-2) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libglib2.0-0t64:amd64 (2.82.2-2) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b2) ... Removing openssl (3.3.2-2) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3-fonttools (4.54.1-4) ... Removing python3-scipy (1.13.1-5) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-3+b1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing python3-lxml:amd64 (5.3.0-1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing python3-fs (2.4.16-4) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b5) ... Removing python3-decorator (5.1.1-5) ... Removing python3-lz4 (4.0.2+dfsg-1+b4) ... Removing python3-sympy (1.13.3-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-six (1.16.0-7) ... Removing python3-tz (2024.1-2) ... Removing python3-unicodedata2 (15.1.0+ds-1+b2) ... Removing unicode-data (15.1.0-1) ... Removing libblas3:amd64 (3.12.0-3+b1) ... Removing python3-pkg-resources (75.2.0-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3 (3.12.6-1) ... Removing python3.12 (3.12.7-2) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12-minimal (3.12.7-2) ... Removing libexpat1:amd64 (2.6.3-2) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 3m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cutadapt', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libapache-pom-java', 'libapparmor1:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0t64:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libmjson-java', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'megadepth', 'mesa-libgallium:amd64', 'multiqc', 'ncbi-vdb-data', 'netbase', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'pigz', 'procps', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-defusedxml', 'python3-dnaio', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-humanize', 'python3-idna', 'python3-imagesize', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-plotly', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pyaml-env', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pysam', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yte', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-backports', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-boot', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-car', 'r-cran-cardata', 'r-cran-caret', 'r-cran-cellranger', 'r-cran-class', 'r-cran-cli', 'r-cran-clipr', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-colourpicker', 'r-cran-commonmark', 'r-cran-conquer', 'r-cran-corrplot', 'r-cran-cowplot', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-data.table', 'r-cran-deriv', 'r-cran-diagram', 'r-cran-digest', 'r-cran-doby', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-e1071', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-forcats', 'r-cran-foreach', 'r-cran-foreign', 'r-cran-formatr', 'r-cran-formula', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-ggpubr', 'r-cran-ggrepel', 'r-cran-ggsci', 'r-cran-ggsignif', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gprofiler2', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-haven', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lme4', 'r-cran-locfit', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-microbenchmark', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', 'r-cran-modelr', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nloptr', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-openssl', 'r-cran-openxlsx', 'r-cran-parallelly', 'r-cran-pbkrtest', 'r-cran-pheatmap', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-polynom', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shape', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tinytex', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-writexl', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 3m4.2s INFO: Running scripts post_remove 3m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_remove_exceptions'] 3m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_remove_exceptions'] 3m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cutadapt', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libapache-pom-java', 'libapparmor1:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0t64:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libmjson-java', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'megadepth', 'mesa-libgallium:amd64', 'multiqc', 'ncbi-vdb-data', 'netbase', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'pigz', 'procps', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-defusedxml', 'python3-dnaio', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-humanize', 'python3-idna', 'python3-imagesize', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-plotly', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pyaml-env', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pysam', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yte', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-backports', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-boot', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-car', 'r-cran-cardata', 'r-cran-caret', 'r-cran-cellranger', 'r-cran-class', 'r-cran-cli', 'r-cran-clipr', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-colourpicker', 'r-cran-commonmark', 'r-cran-conquer', 'r-cran-corrplot', 'r-cran-cowplot', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-data.table', 'r-cran-deriv', 'r-cran-diagram', 'r-cran-digest', 'r-cran-doby', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-e1071', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-forcats', 'r-cran-foreach', 'r-cran-foreign', 'r-cran-formatr', 'r-cran-formula', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-ggpubr', 'r-cran-ggrepel', 'r-cran-ggsci', 'r-cran-ggsignif', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gprofiler2', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-haven', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lme4', 'r-cran-locfit', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-microbenchmark', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', 'r-cran-modelr', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nloptr', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-openssl', 'r-cran-openxlsx', 'r-cran-parallelly', 'r-cran-pbkrtest', 'r-cran-pheatmap', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-polynom', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shape', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tinytex', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-writexl', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 3m4.6s DUMP: (Reading database ... 5306 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for adwaita-icon-theme (47.0-2) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. 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which isn't installed dpkg: warning: ignoring request to remove r-cran-zip which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove salmon which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for shared-mime-info (2.4-5+b1) ... dpkg: warning: ignoring request to remove snakemake which isn't installed dpkg: warning: ignoring request to remove sphinx-common which isn't installed Purging configuration files for systemd (257~rc1-3) ... dpkg: warning: ignoring request to remove systemd-sysv which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove trim-galore which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xkb-data which isn't installed Purging configuration files for xml-core (0.19) ... dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3.1:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cutadapt', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libapache-pom-java', 'libapparmor1:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0t64:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libmjson-java', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'megadepth', 'mesa-libgallium:amd64', 'multiqc', 'ncbi-vdb-data', 'netbase', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'pigz', 'procps', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-defusedxml', 'python3-dnaio', 'python3-docutils', 'python3-dpath', 'python3-fastjsonschema', 'python3-fonttools', 'python3-fs', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-humanize', 'python3-idna', 'python3-imagesize', 'python3-importlib-metadata', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-jinja2', 'python3-jsonschema', 'python3-jsonschema-specifications', 'python3-jupyter-core', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plac', 'python3-platformdirs', 'python3-plotly', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pyaml-env', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pysam', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-traitlets', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yte', 'python3-zipp', 'python3.12', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-backports', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-boot', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-car', 'r-cran-cardata', 'r-cran-caret', 'r-cran-cellranger', 'r-cran-class', 'r-cran-cli', 'r-cran-clipr', 'r-cran-clock', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-colourpicker', 'r-cran-commonmark', 'r-cran-conquer', 'r-cran-corrplot', 'r-cran-cowplot', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-data.table', 'r-cran-deriv', 'r-cran-diagram', 'r-cran-digest', 'r-cran-doby', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-e1071', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-forcats', 'r-cran-foreach', 'r-cran-foreign', 'r-cran-formatr', 'r-cran-formula', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-future', 'r-cran-future.apply', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-ggpubr', 'r-cran-ggrepel', 'r-cran-ggsci', 'r-cran-ggsignif', 'r-cran-globals', 'r-cran-glue', 'r-cran-gower', 'r-cran-gprofiler2', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hardhat', 'r-cran-haven', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-ipred', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lava', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-listenv', 'r-cran-littler', 'r-cran-lme4', 'r-cran-locfit', 'r-cran-lubridate', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-microbenchmark', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', 'r-cran-modelr', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-nloptr', 'r-cran-nnet', 'r-cran-numderiv', 'r-cran-openssl', 'r-cran-openxlsx', 'r-cran-parallelly', 'r-cran-pbkrtest', 'r-cran-pheatmap', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-polynom', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shape', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-timechange', 'r-cran-timedate', 'r-cran-tinytex', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-writexl', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 3m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', 'pigx-rnaseq'] 3m4.6s DUMP: dpkg: warning: ignoring request to remove pigx-rnaseq which isn't installed 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', 'pigx-rnaseq'] 3m4.6s INFO: Running scripts post_purge 3m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_purge_exceptions'] 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_purge_exceptions'] 3m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', '--pending'] 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--purge', '--pending'] 3m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--remove', '--pending'] 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg', '--remove', '--pending'] 3m4.6s INFO: Running scripts post_test 3m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_test_exceptions'] 3m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'tmp/scripts/post_test_exceptions'] 3m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 3m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 3m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-divert', '--list'] 3m4.8s DUMP: 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 /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 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 /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 3m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'dpkg-divert', '--list'] 3m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'clean'] 3m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x', 'apt-get', 'clean'] 3m5.0s DEBUG: Recording chroot state 3m5.2s INFO: Warning: Package purging left files on system: /etc/default/locale -> ../locale.conf not owned /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /etc/vconsole.conf -> default/keyboard not owned /root/.ssh/ not owned /var/cache/private/ not owned /var/lib/private/ not owned /var/log/private/ not owned 3m5.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/shm'] 3m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/shm'] 3m5.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/console'] 3m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/console'] 3m5.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/ptmx'] 3m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/ptmx'] 3m5.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/pts'] 3m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/dev/pts'] 3m5.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/proc'] 3m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x/proc'] 3m5.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 3m5.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpdmez5w6x'] 3m5.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpdmez5w6x 3m5.6s INFO: PASS: Upgrading between Debian distributions. 3m5.6s INFO: PASS: All tests. 3m5.6s INFO: piuparts run ends. ret=0 End: 2024-11-07 15:25:02 GMT