Start: 2025-04-09 18:12:04 GMT 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/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt pigx-rnaseq=0.1.1-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmps0rc_fks 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmps0rc_fks 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/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/tmps0rc_fks/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/tmps0rc_fks/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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/tmps0rc_fks/tmp/scripts/ 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmps0rc_fks/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'update'] 0m2.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7417 kB] Fetched 17.8 MB in 1s (12.4 MB/s) Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bash coreutils libssl3t64 openssl-provider-legacy 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7251 kB of archives. After this operation, 824 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-2 [1500 kB] Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB] Get:3 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB] Fetched 7251 kB in 0s (65.7 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 ... 4927 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-2_amd64.deb ... Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ... Setting up bash (5.2.37-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../coreutils_9.7-1_amd64.deb ... Unpacking coreutils (9.7-1) over (9.6-2) ... Setting up coreutils (9.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.0-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.0-1) over (3.4.1-1) ... Setting up openssl-provider-legacy (3.5.0-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4926 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.0-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.0-1) over (3.4.1-1) ... Setting up libssl3t64:amd64 (3.5.0-1) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.41-6) ... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-yf', 'dist-upgrade'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 31e44ff00e610efb534d9d62a0a21228 - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s 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 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_fake-essential'] 0m4.5s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Reading state information... init-system-helpers is already the newest version (1.68). The following additional packages will be installed: libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks Recommended packages: libgpm2 psmisc linux-sysctl-defaults The following NEW packages will be installed: dbconfig-common libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 1757 kB of archives. After this operation, 4947 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:6 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:7 http://deb.debian.org/debian sid/main amd64 ucf all 3.0051 [42.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB] Preconfiguring packages ... Fetched 1757 kB in 0s (23.1 MB/s) Selecting previously unselected package libncursesw6: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 ... 4925 files and directories currently installed.) Preparing to unpack .../0-libncursesw6_6.5+20250216-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-2) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-7_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-7_amd64.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libtext-charwidth-perl:amd64. Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b4_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../5-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../6-ucf_3.0051_all.deb ... Moving old data out of the way Unpacking ucf (3.0051) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../7-dbconfig-common_2.0.24_all.deb ... Unpacking dbconfig-common (2.0.24) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libproc2-0:amd64 (2:4.0.4-7) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up sensible-utils (0.0.24) ... Setting up procps (2:4.0.4-7) ... Setting up ucf (3.0051) ... Setting up dbconfig-common (2.0.24) ... Creating config file /etc/dbconfig-common/config with new version Processing triggers for libc-bin (2.41-6) ... 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_fake-essential'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_forbid_home'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 0m4.5s DEBUG: Recording chroot state 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed coreutils coreutils 9.7-1 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-3 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-3 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 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-3 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed procps procps 2:4.0.4-7 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-1 install ok installed ucf ucf 3.0051 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-divert', '--list'] 0m4.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 /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 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-divert', '--list'] 0m4.8s INFO: Running scripts is_testable 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/is_testable_uninstallable'] 0m4.8s INFO: apt-cache does not know about any of the requested packages 0m4.8s INFO: Running scripts pre_test 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_test_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_test_root_password'] 0m4.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_test_root_password'] 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 0m5.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 0m5.2s DEBUG: No broken symlinks as far as we can find. 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq=0.1.1-1'] 0m5.8s 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 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq=0.1.1-1'] 0m5.8s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team 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 Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m5.8s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp8vos6ae3/piuparts-depends-dummy'] 0m5.8s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp8vos6ae3/piuparts-depends-dummy.deb'. 0m5.8s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp8vos6ae3/piuparts-depends-dummy'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.8s DUMP: 3.0.0 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m5.8s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp8vos6ae3/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmps0rc_fks/tmp 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 1m10.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: 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 junit4 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 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-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 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libezmorph-java libffi8 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu76 libidn2-0 libimagequant0 libisal2 libitm1 libjaxen-java 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-java libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnspr4 libnss3 libnuma1 libopenjp2-7 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtasn1-6 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 libzopfli1 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 python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click 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-numpy-dev 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-pytz python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy 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-zopfli python3.13 python3.13-minimal 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-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 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-sparsevctrs 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 sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev Suggested packages: adwaita-icon-theme-legacy blt-demo gettext-base 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 libcommons-collections3-java-doc libcommons-collections4-java-doc libasm-java libxz-java libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common rng-tools gdbm-l10n low-memory-monitor gnutls-bin krb5-doc krb5-user gvfs picard-tools libhwloc-contrib-plugins libdom4j-java libjdom1-java 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 libxerces2-java-doc libxml-commons-resolver1.1-java-doc libxom-java-doc 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 python-jupyter-core-doc python3-pip python-lxml-doc python-markdown-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 gir1.2-gtk-4.0 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 latexmk node-mathjax-full 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 python3.13-venv python3.13-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-hdf5array r-bioc-pwalign 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-bsgenome r-bioc-genomicfeatures r-cran-covr 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-txdbmaker 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-experimenthub r-bioc-rhdf5 r-bioc-singlecellexperiment r-cran-dbi r-cran-rmariadb r-cran-rstudioapi r-cran-ragg r-cran-vdiffr r-cran-magick r-cran-sf r-cran-getopt r-cran-interp r-cran-gam r-cran-multcomp r-cran-roxygen2 r-cran-inline r-cran-tinytest r-cran-rmpi r-cran-rlecuyer 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 libgpg-error-l10n 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 python3-fqdn python3-isoduration python3-json-pointer python3-rfc3339-validator python3-rfc3986-validator python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-cssselect python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-olefile g++ | c++-compiler python3-pooch python3-boto3 python3-paramiko python3-zstandard make isympy-common python3-isal r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-roxygen2 r-cran-markdown r-cran-ff 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-bradleyterry2 r-cran-earth r-cran-ellipse r-cran-fastica r-cran-kernlab r-cran-mda r-cran-mlbench r-cran-mlmetrics r-cran-party r-cran-pls r-cran-randomforest r-cran-rann r-cran-themis r-cran-callr 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-mockery r-cran-webutils r-cran-xts r-cran-dbi r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-testit w3m | www-browser r-cran-pkgload r-cran-unitizer r-cran-rsvg r-cran-rhpcblasctl r-cran-r.rsp 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-tinytest r-cran-usethis r-cran-th.data r-cran-gridsvg r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-webshot node-highlight.js r-cran-fields r-bioc-graph r-cran-igraph r-cran-lavasearch2 r-cran-mets r-cran-optimx r-cran-polycor r-cran-visnetwork r-cran-lintr r-cran-tidyverse r-cran-r.devices r-cran-sodium r-cran-diagrammer r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-ggthemes r-cran-ggally r-cran-ggalluvial r-cran-dendextend r-cran-irdisplay r-cran-rversions r-cran-doparallel r-cran-itertools r-cran-logcondens r-cran-pbmcapply r-cran-furrr r-cran-cba r-cran-gbrd r-cran-ddalpha r-cran-dials 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-blob r-cran-here r-cran-pkgbuild 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 linux-sysctl-defaults 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: 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 junit4 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 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-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 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libezmorph-java libffi8 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu76 libidn2-0 libimagequant0 libisal2 libitm1 libjaxen-java 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-java libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnspr4 libnss3 libnuma1 libopenjp2-7 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtasn1-6 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 libzopfli1 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 piuparts-depends-dummy python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click 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-numpy-dev 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-pytz python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy 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-zopfli python3.13 python3.13-minimal 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-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 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-sparsevctrs 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 sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev 0 upgraded, 665 newly installed, 0 to remove and 0 not upgraded. Need to get 619 MB/619 MB of archives. After this operation, 2290 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [858 B] Get:2 http://deb.debian.org/debian sid/main amd64 libsystemd-shared amd64 257.5-2 [2142 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libapparmor1 amd64 4.1.0~beta5-6 [43.5 kB] Get:4 http://deb.debian.org/debian sid/main amd64 systemd amd64 257.5-2 [3091 kB] Get:5 http://deb.debian.org/debian sid/main amd64 systemd-sysv amd64 257.5-2 [63.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get:7 http://deb.debian.org/debian sid/main amd64 dbus-bin amd64 1.16.2-2 [80.0 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:10 http://deb.debian.org/debian sid/main amd64 dbus-daemon amd64 1.16.2-2 [159 kB] Get:11 http://deb.debian.org/debian sid/main amd64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 dbus amd64 1.16.2-2 [71.6 kB] Get:13 http://deb.debian.org/debian sid/main amd64 pigz amd64 2.8-1 [62.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.3-1 [861 kB] Get:15 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.3-1 [2210 kB] Get:16 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.3-1 [27.2 kB] Get:17 http://deb.debian.org/debian sid/main amd64 media-types all 13.0.0 [29.3 kB] Get:18 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get:20 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.3-1 [1954 kB] Get:23 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.3-1 [751 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.3-1 [10.2 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.3-1 [28.2 kB] Get:26 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:29 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:30 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:31 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:32 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.0-1 [1491 kB] Get:33 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libpam-systemd amd64 257.5-2 [296 kB] Get:35 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.1-2 [3017 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.1-2 [4315 kB] Get:39 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.1-2 [267 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:42 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Get:44 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-5+b2 [760 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:49 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-2 [140 kB] Get:54 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 4.18.4+ds-1 [51.7 kB] Get:55 http://deb.debian.org/debian sid/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get:56 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 48.0-1 [504 kB] Get:57 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.56.1-2 [171 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:61 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:62 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:63 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:73 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+24 [217 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:76 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get:77 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get:78 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:79 http://deb.debian.org/debian sid/main amd64 coinor-libcoinutils3v5 amd64 2.11.11+ds-5 [460 kB] Get:80 http://deb.debian.org/debian sid/main amd64 coinor-libosi1v5 amd64 0.108.10+ds-2 [293 kB] Get:81 http://deb.debian.org/debian sid/main amd64 coinor-libclp1 amd64 1.17.10+ds-1 [883 kB] Get:82 http://deb.debian.org/debian sid/main amd64 coinor-libcgl1 amd64 0.60.9+ds-1 [426 kB] Get:83 http://deb.debian.org/debian sid/main amd64 coinor-libcbc3.1 amd64 2.10.12+ds-1 [714 kB] Get:84 http://deb.debian.org/debian sid/main amd64 coinor-cbc amd64 2.10.12+ds-1 [16.2 kB] Get:85 http://deb.debian.org/debian sid/main amd64 python3-xopen all 1.7.0-3 [16.8 kB] Get:86 http://deb.debian.org/debian sid/main amd64 python3-dnaio amd64 1.2.3-1+b1 [84.6 kB] Get:87 http://deb.debian.org/debian sid/main amd64 python3-cutadapt amd64 4.7-2+b3 [204 kB] Get:88 http://deb.debian.org/debian sid/main amd64 cutadapt all 4.7-2 [25.1 kB] Get:89 http://deb.debian.org/debian sid/main amd64 dbus-user-session amd64 1.16.2-2 [52.1 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get:91 http://deb.debian.org/debian sid/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get:92 http://deb.debian.org/debian sid/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get:93 http://deb.debian.org/debian sid/main amd64 java-common all 0.76 [6776 B] Get:94 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.110-1 [1393 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.3.3-1 [55.2 kB] Get:98 http://deb.debian.org/debian sid/main amd64 openjdk-21-jre-headless amd64 21.0.7~8ea-1 [41.8 MB] Get:99 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:100 http://deb.debian.org/debian sid/main amd64 libatk1.0-0t64 amd64 2.56.1-2 [51.6 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libatspi2.0-0t64 amd64 2.56.1-2 [80.6 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libatk-bridge2.0-0t64 amd64 2.56.1-2 [68.4 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libcairo-gobject2 amd64 1.18.4-1+b1 [130 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libcloudproviders0 amd64 0.3.6-2 [29.2 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libcolord2 amd64 1.4.7-3 [139 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-16 [112 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-5 [9316 B] Get:123 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:130 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libwayland-client0 amd64 1.23.1-3 [26.8 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libwayland-cursor0 amd64 1.23.1-3 [11.9 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libwayland-egl1 amd64 1.23.1-3 [5860 B] Get:140 http://deb.debian.org/debian sid/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libxinerama1 amd64 2:1.1.4-3+b4 [16.0 kB] Get:145 http://deb.debian.org/debian sid/main amd64 xkb-data all 2.42-1 [790 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libxkbcommon0 amd64 1.7.0-2 [113 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libgtk-3-common all 3.24.49-3 [4908 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libgtk-3-0t64 amd64 3.24.49-3 [2769 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get:152 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.124-2 [64.1 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libllvm19 amd64 1:19.1.7-3 [26.0 MB] Get:166 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get:171 http://deb.debian.org/debian sid/main amd64 mesa-libgallium amd64 25.0.3-1 [9624 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libwayland-server0 amd64 1.23.1-3 [34.4 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libgbm1 amd64 25.0.3-1 [44.2 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.4.309.0-1 [130 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 25.0.3-1 [45.7 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 25.0.3-1 [143 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.13-1 [21.1 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libasound2t64 amd64 1.2.13-1+b1 [373 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get:183 http://deb.debian.org/debian sid/main amd64 openjdk-21-jre amd64 21.0.7~8ea-1 [205 kB] Get:184 http://deb.debian.org/debian sid/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:185 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:186 http://deb.debian.org/debian sid/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libisal2 amd64 2.31.1-1.1 [114 kB] Get:188 http://deb.debian.org/debian sid/main amd64 fastp amd64 0.24.0+dfsg-1 [219 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libcommons-math3-java all 3.6.1-4 [2040 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libapache-pom-java all 33-2 [5852 B] Get:192 http://deb.debian.org/debian sid/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libcommons-codec-java all 1.18.0-1 [304 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libcommons-io-java all 2.18.0-1 [509 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get:199 http://deb.debian.org/debian sid/main amd64 junit4 all 4.13.2-5 [350 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libxom-java all 1.3.9-1 [174 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB] Get:215 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7.1 [156 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.9+dfsg-7.1 [25.6 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.9+dfsg-7.1 [112 kB] Get:220 http://deb.debian.org/debian sid/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.2.2-1 [29.3 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B] Get:223 http://deb.debian.org/debian sid/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:226 http://deb.debian.org/debian sid/main amd64 fastqc all 0.12.1+dfsg-4 [398 kB] Get:227 http://deb.debian.org/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:228 http://deb.debian.org/debian sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:229 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get:230 http://deb.debian.org/debian sid/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:239 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Get:242 http://deb.debian.org/debian sid/main amd64 liberror-perl all 0.17030-1 [26.9 kB] Get:243 http://deb.debian.org/debian sid/main amd64 git-man all 1:2.49.0-1 [2236 kB] Get:244 http://deb.debian.org/debian sid/main amd64 git amd64 1:2.49.0-1 [9059 kB] Get:245 http://deb.debian.org/debian sid/main amd64 hisat2 amd64 2.2.1-5+b3 [3797 kB] Get:246 http://deb.debian.org/debian sid/main amd64 javascript-common all 12 [5236 B] Get:247 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libbigwig0t64 amd64 0.4.7+dfsg-3.1+b2 [28.7 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Get:251 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Get:253 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Get:254 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Get:255 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Get:257 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.41-6 [57.0 kB] Get:258 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.21-1 [2542 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Get:260 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:261 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.41-6 [1988 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get:264 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:265 http://deb.debian.org/debian sid/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.2 [282 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2 [254 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Get:268 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB] Get:269 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB] Get:270 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:271 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:272 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:273 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB] Get:274 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:275 http://deb.debian.org/debian sid/main amd64 libicu76 amd64 76.1-3 [9721 kB] Get:276 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:277 http://deb.debian.org/debian sid/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get:278 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:279 http://deb.debian.org/debian sid/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:280 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:281 http://deb.debian.org/debian sid/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:282 http://deb.debian.org/debian sid/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:283 http://deb.debian.org/debian sid/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:284 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:285 http://deb.debian.org/debian sid/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:286 http://deb.debian.org/debian sid/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get:287 http://deb.debian.org/debian sid/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get:288 http://deb.debian.org/debian sid/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:289 http://deb.debian.org/debian sid/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:290 http://deb.debian.org/debian sid/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:291 http://deb.debian.org/debian sid/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get:292 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:293 http://deb.debian.org/debian sid/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:294 http://deb.debian.org/debian sid/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:295 http://deb.debian.org/debian sid/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:296 http://deb.debian.org/debian sid/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:297 http://deb.debian.org/debian sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:298 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get:299 http://deb.debian.org/debian sid/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:300 http://deb.debian.org/debian sid/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:301 http://deb.debian.org/debian sid/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB] Get:302 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:303 http://deb.debian.org/debian sid/main amd64 libnlopt0 amd64 2.7.1-6+b4 [178 kB] Get:304 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:305 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB] Get:306 http://deb.debian.org/debian sid/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get:307 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get:308 http://deb.debian.org/debian sid/main amd64 libpython3.13 amd64 3.13.3-1 [2156 kB] Get:309 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:310 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get:311 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get:312 http://deb.debian.org/debian sid/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get:313 http://deb.debian.org/debian sid/main amd64 libtbbbind-2-5 amd64 2022.1.0-1 [14.0 kB] Get:314 http://deb.debian.org/debian sid/main amd64 libtbbmalloc2 amd64 2022.1.0-1 [50.2 kB] Get:315 http://deb.debian.org/debian sid/main amd64 libtbb12 amd64 2022.1.0-1 [91.7 kB] Get:316 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get:317 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB] Get:318 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:319 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get:320 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get:321 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1.2 [233 kB] Get:322 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:323 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:324 http://deb.debian.org/debian sid/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get:325 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB] Get:326 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-29 [173 kB] Get:327 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:328 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.3-1+b1 [28.3 MB] Get:329 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.21-1 [107 kB] Get:330 http://deb.debian.org/debian sid/main amd64 littler all 0.3.21-1 [16.9 kB] Get:331 http://deb.debian.org/debian sid/main amd64 megadepth amd64 1.2.0-4+b1 [83.0 kB] Get:332 http://deb.debian.org/debian sid/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB] Get:333 http://deb.debian.org/debian sid/main amd64 python3-humanfriendly all 10.0-6 [85.6 kB] Get:334 http://deb.debian.org/debian sid/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:335 http://deb.debian.org/debian sid/main amd64 python3-humanize all 4.12.1-1 [52.9 kB] Get:336 http://deb.debian.org/debian sid/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get:337 http://deb.debian.org/debian sid/main amd64 python3-importlib-metadata all 8.6.1-1 [21.4 kB] Get:338 http://deb.debian.org/debian sid/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get:339 http://deb.debian.org/debian sid/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Get:340 http://deb.debian.org/debian sid/main amd64 python3-markdown all 3.7-2 [85.2 kB] Get:341 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.10.1+dfsg1-2 [2736 kB] Get:342 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get:343 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 11.1.0-5+b1 [513 kB] Get:344 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.3-1 [107 kB] Get:345 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.13.3-1 [9548 B] Get:346 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 11.1.0-5+b1 [81.6 kB] Get:347 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:348 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.3.1-1+b1 [216 kB] Get:349 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:350 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get:351 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.7-1 [16.6 kB] Get:352 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-7 [95.2 kB] Get:353 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.3.2-1 [1297 kB] Get:354 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.4.0+dfsg-2 [25.3 kB] Get:355 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.2.1-1 [32.9 kB] Get:356 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.15.2-7 [16.3 MB] Get:357 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:358 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-5 [4148 kB] Get:359 http://deb.debian.org/debian sid/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get:360 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get:361 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b4 [299 kB] Get:362 http://deb.debian.org/debian sid/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get:363 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:364 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.57.0-1 [1438 kB] Get:365 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get:366 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get:367 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-2 [23.8 MB] Get:368 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get:369 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get:370 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.10-1 [42.0 kB] Get:371 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Get:372 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get:373 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Get:374 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.2-1 [151 kB] Get:375 http://deb.debian.org/debian sid/main amd64 python3-tz all 2025.2-1 [4072 B] Get:376 http://deb.debian.org/debian sid/main amd64 python3-fastjsonschema all 2.21.1-1 [22.4 kB] Get:377 http://deb.debian.org/debian sid/main amd64 python3-rpds-py amd64 0.21.0-2+b1 [257 kB] Get:378 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.13.1-1 [90.2 kB] Get:379 http://deb.debian.org/debian sid/main amd64 python3-referencing all 0.36.2-1 [23.7 kB] Get:380 http://deb.debian.org/debian sid/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get:381 http://deb.debian.org/debian sid/main amd64 python3-jsonschema all 4.19.2-6 [71.4 kB] Get:382 http://deb.debian.org/debian sid/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get:383 http://deb.debian.org/debian sid/main amd64 python3-jupyter-core all 5.7.2-5 [35.3 kB] Get:384 http://deb.debian.org/debian sid/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get:385 http://deb.debian.org/debian sid/main amd64 python3-tenacity all 8.4.2+really8.4.1-2 [46.0 kB] Get:386 http://deb.debian.org/debian sid/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get:387 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get:388 http://deb.debian.org/debian sid/main amd64 python3-pyaml-env all 1.2.1-2 [9032 B] Get:389 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get:390 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get:391 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get:392 http://deb.debian.org/debian sid/main amd64 python3-rich all 13.9.4-1 [203 kB] Get:393 http://deb.debian.org/debian sid/main amd64 python3-rich-click all 1.6.0-2 [21.2 kB] Get:394 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:395 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get:396 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get:397 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:398 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get:399 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:400 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get:401 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get:402 http://deb.debian.org/debian sid/main amd64 python3-colormath all 3.0.0-4 [34.7 kB] Get:403 http://deb.debian.org/debian sid/main amd64 python3-spectra all 0.1.0-1 [16.6 kB] Get:404 http://deb.debian.org/debian sid/main amd64 python3-lzstring all 1.0.4-3 [5544 B] Get:405 http://deb.debian.org/debian sid/main amd64 multiqc all 1.21+dfsg-2 [781 kB] Get:406 http://deb.debian.org/debian sid/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:407 http://deb.debian.org/debian sid/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:408 http://deb.debian.org/debian sid/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:409 http://deb.debian.org/debian sid/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:410 http://deb.debian.org/debian sid/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get:411 http://deb.debian.org/debian sid/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get:412 http://deb.debian.org/debian sid/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get:413 http://deb.debian.org/debian sid/main amd64 python3-babel all 2.17.0-1 [117 kB] Get:414 http://deb.debian.org/debian sid/main amd64 python3-configargparse all 1.7-2 [31.4 kB] Get:415 http://deb.debian.org/debian sid/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get:416 http://deb.debian.org/debian sid/main amd64 python3-datrie amd64 0.8.2-5+b2 [129 kB] Get:417 http://deb.debian.org/debian sid/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b11 [52.2 kB] Get:418 http://deb.debian.org/debian sid/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get:419 http://deb.debian.org/debian sid/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get:420 http://deb.debian.org/debian sid/main amd64 python3-roman all 5.0-1 [10.6 kB] Get:421 http://deb.debian.org/debian sid/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:422 http://deb.debian.org/debian sid/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:423 http://deb.debian.org/debian sid/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get:424 http://deb.debian.org/debian sid/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get:425 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get:426 http://deb.debian.org/debian sid/main amd64 python3-numpydoc all 1.8.0-1 [51.4 kB] Get:427 http://deb.debian.org/debian sid/main amd64 python3-py2bit amd64 0.3.3-1+b1 [21.4 kB] Get:428 http://deb.debian.org/debian sid/main amd64 python3-pybigwig amd64 0.3.23+dfsg-1+b3 [37.8 kB] Get:429 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get:430 http://deb.debian.org/debian sid/main amd64 python3-deeptools all 3.5.6+dfsg-1 [150 kB] Get:431 http://deb.debian.org/debian sid/main amd64 python3-dpath all 2.2.0-1 [19.9 kB] Get:432 http://deb.debian.org/debian sid/main amd64 python3-smmap all 6.0.0-1 [20.1 kB] Get:433 http://deb.debian.org/debian sid/main amd64 python3-gitdb all 4.0.12-1 [45.8 kB] Get:434 http://deb.debian.org/debian sid/main amd64 python3-git all 3.1.44-1 [147 kB] Get:435 http://deb.debian.org/debian sid/main amd64 python3-htseq amd64 2.0.9+dfsg-1+b2 [321 kB] Get:436 http://deb.debian.org/debian sid/main amd64 python3-plac all 1.4.3-2 [65.7 kB] Get:437 http://deb.debian.org/debian sid/main amd64 python3-psutil amd64 7.0.0-1 [220 kB] Get:438 http://deb.debian.org/debian sid/main amd64 python3-pulp all 2.7.0+dfsg-4 [72.4 kB] Get:439 http://deb.debian.org/debian sid/main amd64 python3-py all 1.11.0-4 [88.8 kB] Get:440 http://deb.debian.org/debian sid/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get:441 http://deb.debian.org/debian sid/main amd64 python3-retry all 0.9.2-3 [7088 B] Get:442 http://deb.debian.org/debian sid/main amd64 python3-wrapt amd64 1.15.0-4+b1 [43.6 kB] Get:443 http://deb.debian.org/debian sid/main amd64 python3-smart-open all 7.1.0-1 [98.7 kB] Get:444 http://deb.debian.org/debian sid/main amd64 python3-stopit all 1.1.2-3 [12.8 kB] Get:445 http://deb.debian.org/debian sid/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:446 http://deb.debian.org/debian sid/main amd64 python3-toposort all 1.10-2 [7336 B] Get:447 http://deb.debian.org/debian sid/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get:448 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB] Get:449 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB] Get:450 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB] Get:451 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.16.0+dfsg-2 [210 kB] Get:452 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:453 http://deb.debian.org/debian sid/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:454 http://deb.debian.org/debian sid/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:455 http://deb.debian.org/debian sid/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:456 http://deb.debian.org/debian sid/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:457 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:458 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:459 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.2-1 [226 kB] Get:460 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.40.0-2 [1326 kB] Get:461 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.40.1-2 [2309 kB] Get:462 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:463 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B] Get:464 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB] Get:465 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 6.2.1+dfsg-1 [195 kB] Get:466 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [445 kB] Get:467 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:468 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:469 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:470 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [402 kB] Get:471 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.6.1-1 [106 kB] Get:472 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:473 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB] Get:474 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] Get:475 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3848 kB] Get:476 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.3-1 [165 kB] Get:477 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.4 MB] Get:478 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-7-1 [1418 kB] Get:479 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-3-1 [4048 kB] Get:480 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.5.0-1 [502 kB] Get:481 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.18.1-1 [449 kB] Get:482 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:483 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [702 kB] Get:484 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1372 kB] Get:485 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2076 kB] Get:486 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2092 kB] Get:487 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1116 kB] Get:488 http://deb.debian.org/debian sid/main amd64 r-cran-locfit amd64 1.5-9.12-1 [513 kB] Get:489 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.4-1 [1370 kB] Get:490 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:491 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB] Get:492 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:493 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:494 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:495 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-65-1 [1113 kB] Get:496 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.168-1 [2329 kB] Get:497 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-3-1 [3378 kB] Get:498 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:499 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:500 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:501 http://deb.debian.org/debian sid/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:502 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:503 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:504 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:505 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.6-1 [629 kB] Get:506 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:507 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:508 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:509 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get:510 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:511 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get:512 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:513 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:514 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:515 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get:516 http://deb.debian.org/debian sid/main amd64 r-cran-rcpparmadillo amd64 14.4.1-1-1 [868 kB] Get:517 http://deb.debian.org/debian sid/main amd64 r-bioc-deseq2 amd64 1.46.0+dfsg-2 [1287 kB] Get:518 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.0-9-1 [30.7 kB] Get:519 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1335 kB] Get:520 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3600 kB] Get:521 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2161 kB] Get:522 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.18-1 [1762 kB] Get:523 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:524 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:525 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:526 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:527 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.66.0-2 [5213 kB] Get:528 http://deb.debian.org/debian sid/main amd64 r-bioc-tximport all 1.34.0+dfsg-2 [91.2 kB] Get:529 http://deb.debian.org/debian sid/main amd64 r-cran-backports amd64 1.5.0-2 [121 kB] Get:530 http://deb.debian.org/debian sid/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:531 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.6.0+dfsg-1 [455 kB] Get:532 http://deb.debian.org/debian sid/main amd64 r-cran-bit64 amd64 4.6.0-1-1 [481 kB] Get:533 http://deb.debian.org/debian sid/main amd64 r-cran-boot all 1.3-31-1 [639 kB] Get:534 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:535 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:536 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-4 [1543 kB] Get:537 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.4-1 [556 kB] Get:538 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.4-1+b1 [896 kB] Get:539 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:540 http://deb.debian.org/debian sid/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:541 http://deb.debian.org/debian sid/main amd64 r-cran-broom all 1.0.7+dfsg-1 [1846 kB] Get:542 http://deb.debian.org/debian sid/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:543 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:544 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:545 http://deb.debian.org/debian sid/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:546 http://deb.debian.org/debian sid/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:547 http://deb.debian.org/debian sid/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:548 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.5+dfsg-1 [248 kB] Get:549 http://deb.debian.org/debian sid/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:550 http://deb.debian.org/debian sid/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:551 http://deb.debian.org/debian sid/main amd64 r-cran-bslib all 0.9.0+dfsg-1 [4664 kB] Get:552 http://deb.debian.org/debian sid/main amd64 r-cran-cardata all 3.0.5-1 [1797 kB] Get:553 http://deb.debian.org/debian sid/main amd64 r-cran-formula all 1.2-5-1 [158 kB] Get:554 http://deb.debian.org/debian sid/main amd64 r-cran-nnet amd64 7.3-20-1 [112 kB] Get:555 http://deb.debian.org/debian sid/main amd64 r-cran-minqa amd64 1.2.8-1 [118 kB] Get:556 http://deb.debian.org/debian sid/main amd64 r-cran-nloptr amd64 2.2.1-2 [254 kB] Get:557 http://deb.debian.org/debian sid/main amd64 r-cran-rbibutils amd64 2.3-1 [948 kB] Get:558 http://deb.debian.org/debian sid/main amd64 r-cran-rdpack all 2.6.3-1 [638 kB] Get:559 http://deb.debian.org/debian sid/main amd64 r-cran-reformulas all 0.4.0-2 [92.2 kB] Get:560 http://deb.debian.org/debian sid/main amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1411 kB] Get:561 http://deb.debian.org/debian sid/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:562 http://deb.debian.org/debian sid/main amd64 r-cran-lme4 amd64 1.1-37-1 [4123 kB] Get:563 http://deb.debian.org/debian sid/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get:564 http://deb.debian.org/debian sid/main amd64 r-cran-cowplot all 1.1.3+dfsg-1 [638 kB] Get:565 http://deb.debian.org/debian sid/main amd64 r-cran-deriv all 4.1.6-1 [151 kB] Get:566 http://deb.debian.org/debian sid/main amd64 r-cran-modelr all 0.1.11-1 [204 kB] Get:567 http://deb.debian.org/debian sid/main amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.1 kB] Get:568 http://deb.debian.org/debian sid/main amd64 r-cran-doby all 4.6.25-1 [4775 kB] Get:569 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 1.0.3-1 [114 kB] Get:570 http://deb.debian.org/debian sid/main amd64 r-cran-xfun amd64 0.51+dfsg-1 [575 kB] Get:571 http://deb.debian.org/debian sid/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:572 http://deb.debian.org/debian sid/main amd64 r-cran-knitr all 1.50+dfsg-1 [843 kB] Get:573 http://deb.debian.org/debian sid/main amd64 r-cran-pbkrtest all 0.5.3-1 [180 kB] Get:574 http://deb.debian.org/debian sid/main amd64 r-cran-sparsem amd64 1.84-2-1+b1 [794 kB] Get:575 http://deb.debian.org/debian sid/main amd64 r-cran-matrixmodels all 0.5-4-1 [354 kB] Get:576 http://deb.debian.org/debian sid/main amd64 r-cran-survival amd64 3.8-3-1 [8265 kB] Get:577 http://deb.debian.org/debian sid/main amd64 r-cran-class amd64 7.3-23-1 [89.7 kB] Get:578 http://deb.debian.org/debian sid/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] Get:579 http://deb.debian.org/debian sid/main amd64 r-cran-e1071 amd64 1.7-16-1 [562 kB] Get:580 http://deb.debian.org/debian sid/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:581 http://deb.debian.org/debian sid/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:582 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2105 kB] Get:583 http://deb.debian.org/debian sid/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB] Get:584 http://deb.debian.org/debian sid/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:585 http://deb.debian.org/debian sid/main amd64 r-cran-proc amd64 1.18.5-1 [987 kB] Get:586 http://deb.debian.org/debian sid/main amd64 r-cran-tzdb amd64 0.5.0-1 [515 kB] Get:587 http://deb.debian.org/debian sid/main amd64 r-cran-clock amd64 0.7.2-1 [1823 kB] Get:588 http://deb.debian.org/debian sid/main amd64 r-cran-gower amd64 1.0.2-1 [209 kB] Get:589 http://deb.debian.org/debian sid/main amd64 r-cran-sparsevctrs amd64 0.2.0-2 [177 kB] Get:590 http://deb.debian.org/debian sid/main amd64 r-cran-hardhat all 1.4.1+dfsg-1 [697 kB] Get:591 http://deb.debian.org/debian sid/main amd64 r-cran-rpart amd64 4.1.24-1 [689 kB] Get:592 http://deb.debian.org/debian sid/main amd64 r-cran-shape all 1.4.6.1-1 [752 kB] Get:593 http://deb.debian.org/debian sid/main amd64 r-cran-diagram all 1.6.5-2 [656 kB] Get:594 http://deb.debian.org/debian sid/main amd64 r-cran-kernsmooth amd64 2.23-26-1 [93.0 kB] Get:595 http://deb.debian.org/debian sid/main amd64 r-cran-globals all 0.16.3-1 [120 kB] Get:596 http://deb.debian.org/debian sid/main amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] Get:597 http://deb.debian.org/debian sid/main amd64 r-cran-parallelly amd64 1.42.0-1 [541 kB] Get:598 http://deb.debian.org/debian sid/main amd64 r-cran-future all 1.34.0+dfsg-1 [649 kB] Get:599 http://deb.debian.org/debian sid/main amd64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] Get:600 http://deb.debian.org/debian sid/main amd64 r-cran-progressr all 0.15.1-1 [352 kB] Get:601 http://deb.debian.org/debian sid/main amd64 r-cran-squarem all 2021.1-1 [179 kB] Get:602 http://deb.debian.org/debian sid/main amd64 r-cran-lava all 1.8.1+dfsg-1 [2230 kB] Get:603 http://deb.debian.org/debian sid/main amd64 r-cran-prodlim amd64 2024.06.25-1 [416 kB] Get:604 http://deb.debian.org/debian sid/main amd64 r-cran-ipred amd64 0.9-15-1 [387 kB] Get:605 http://deb.debian.org/debian sid/main amd64 r-cran-timechange amd64 0.3.0-1 [173 kB] Get:606 http://deb.debian.org/debian sid/main amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1013 kB] Get:607 http://deb.debian.org/debian sid/main amd64 r-cran-timedate amd64 4041.110-1 [1211 kB] Get:608 http://deb.debian.org/debian sid/main amd64 r-cran-recipes all 1.1.0+dfsg-1 [2047 kB] Get:609 http://deb.debian.org/debian sid/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:610 http://deb.debian.org/debian sid/main amd64 r-cran-caret amd64 7.0-1+dfsg-1 [3471 kB] Get:611 http://deb.debian.org/debian sid/main amd64 r-cran-conquer amd64 1.3.3-1 [471 kB] Get:612 http://deb.debian.org/debian sid/main amd64 r-cran-quantreg amd64 6.1-1 [1442 kB] Get:613 http://deb.debian.org/debian sid/main amd64 r-cran-foreign amd64 0.8.90-1 [253 kB] Get:614 http://deb.debian.org/debian sid/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:615 http://deb.debian.org/debian sid/main amd64 r-cran-forcats all 1.0.0-1 [413 kB] Get:616 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:617 http://deb.debian.org/debian sid/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:618 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:619 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:620 http://deb.debian.org/debian sid/main amd64 r-cran-vroom amd64 1.6.5-1 [830 kB] Get:621 http://deb.debian.org/debian sid/main amd64 r-cran-readr amd64 2.1.5-1 [759 kB] Get:622 http://deb.debian.org/debian sid/main amd64 r-cran-haven amd64 2.5.4-1 [342 kB] Get:623 http://deb.debian.org/debian sid/main amd64 r-cran-rematch all 2.0.0-1 [18.2 kB] Get:624 http://deb.debian.org/debian sid/main amd64 r-cran-cellranger all 1.1.0-3 [100 kB] Get:625 http://deb.debian.org/debian sid/main amd64 r-cran-readxl amd64 1.4.5-1 [341 kB] Get:626 http://deb.debian.org/debian sid/main amd64 r-cran-writexl amd64 1.5.3-1 [148 kB] Get:627 http://deb.debian.org/debian sid/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get:628 http://deb.debian.org/debian sid/main amd64 r-cran-r.oo all 1.27.0-1 [983 kB] Get:629 http://deb.debian.org/debian sid/main amd64 r-cran-r.utils all 2.13.0-1 [1433 kB] Get:630 http://deb.debian.org/debian sid/main amd64 r-cran-zip amd64 2.3.2-1 [140 kB] Get:631 http://deb.debian.org/debian sid/main amd64 r-cran-openxlsx amd64 4.2.8-1 [2034 kB] Get:632 http://deb.debian.org/debian sid/main amd64 r-cran-rio all 1.2.3-1 [531 kB] Get:633 http://deb.debian.org/debian sid/main amd64 r-cran-car all 3.1-3-1 [1533 kB] Get:634 http://deb.debian.org/debian sid/main amd64 r-cran-fontawesome all 0.5.3-1 [1311 kB] Get:635 http://deb.debian.org/debian sid/main amd64 r-cran-tinytex all 0.56-1 [149 kB] Get:636 http://deb.debian.org/debian sid/main amd64 r-cran-later amd64 1.4.1+dfsg-1 [141 kB] Get:637 http://deb.debian.org/debian sid/main amd64 r-cran-promises amd64 1.3.2+dfsg-1 [288 kB] Get:638 http://deb.debian.org/debian sid/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:639 http://deb.debian.org/debian sid/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:640 http://deb.debian.org/debian sid/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:641 http://deb.debian.org/debian sid/main amd64 r-cran-commonmark amd64 1.9.5-1 [123 kB] Get:642 http://deb.debian.org/debian sid/main amd64 r-cran-shiny all 1.10.0+dfsg-2 [3139 kB] Get:643 http://deb.debian.org/debian sid/main amd64 r-cran-rmarkdown all 2.29+dfsg-1 [1473 kB] Get:644 http://deb.debian.org/debian sid/main amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] Get:645 http://deb.debian.org/debian sid/main amd64 r-cran-miniui all 0.1.1.1-3 [35.9 kB] Get:646 http://deb.debian.org/debian sid/main amd64 r-cran-shinyjs all 2.1.0-1 [1009 kB] Get:647 http://deb.debian.org/debian sid/main amd64 r-cran-colourpicker all 1.3.0+dfsg-1 [1212 kB] Get:648 http://deb.debian.org/debian sid/main amd64 r-cran-corrplot all 0.95-1 [135 kB] Get:649 http://deb.debian.org/debian sid/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get:650 http://deb.debian.org/debian sid/main amd64 r-cran-crosstalk all 1.2.1+dfsg-1 [175 kB] Get:651 http://deb.debian.org/debian sid/main amd64 r-cran-dt all 0.33+dfsg-1 [248 kB] Get:652 http://deb.debian.org/debian sid/main amd64 r-cran-ggrepel amd64 0.9.6-1 [265 kB] Get:653 http://deb.debian.org/debian sid/main amd64 r-cran-ggsci all 3.2.0-1 [2103 kB] Get:654 http://deb.debian.org/debian sid/main amd64 r-cran-ggsignif all 0.6.4-1 [589 kB] Get:655 http://deb.debian.org/debian sid/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:656 http://deb.debian.org/debian sid/main amd64 r-cran-polynom all 1.4-1+dfsg-1 [92.5 kB] Get:657 http://deb.debian.org/debian sid/main amd64 r-cran-rstatix all 0.7.2-1 [609 kB] Get:658 http://deb.debian.org/debian sid/main amd64 r-cran-ggpubr all 0.6.0-1 [2080 kB] Get:659 http://deb.debian.org/debian sid/main amd64 r-cran-plotly all 4.10.4+dfsg-2 [3634 kB] Get:660 http://deb.debian.org/debian sid/main amd64 r-cran-gprofiler2 all 0.2.3+dfsg-1 [121 kB] Get:661 http://deb.debian.org/debian sid/main amd64 r-cran-pheatmap all 1.0.12-2 [77.9 kB] Get:662 http://deb.debian.org/debian sid/main amd64 salmon amd64 1.10.2+ds1-1+b5 [3421 kB] Get:663 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.21-1 [667 kB] Get:664 http://deb.debian.org/debian sid/main amd64 snakemake all 7.32.4-7 [318 kB] Get:665 http://deb.debian.org/debian sid/main amd64 trim-galore all 0.6.10-1 [17.8 MB] Preconfiguring packages ... Fetched 619 MB in 12s (51.9 MB/s) Selecting previously unselected package libsystemd-shared: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 ... 5473 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257.5-2) ... Selecting previously unselected package libapparmor1:amd64. Preparing to unpack .../libapparmor1_4.1.0~beta5-6_amd64.deb ... Unpacking libapparmor1:amd64 (4.1.0~beta5-6) ... Setting up libsystemd-shared:amd64 (257.5-2) ... Selecting previously unselected package systemd. (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 ... 5486 files and directories currently installed.) Preparing to unpack .../systemd_257.5-2_amd64.deb ... Unpacking systemd (257.5-2) ... Setting up libapparmor1:amd64 (4.1.0~beta5-6) ... Setting up systemd (257.5-2) ... 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:14: 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 ... 6423 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.5-2_amd64.deb ... Unpacking systemd-sysv (257.5-2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../01-libdbus-1-3_1.16.2-2_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.2-2_amd64.deb ... Unpacking dbus-bin (1.16.2-2) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding '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' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding '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' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../6-libpython3.13-stdlib_3.13.3-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../7-python3.13_3.13.3-1_amd64.deb ... Unpacking python3.13 (3.13.3-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libc-dev-bin (2.41-6) ... Setting up python-matplotlib-data (3.10.1+dfsg1-2) ... Setting up openssl (3.5.0-1) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up node-normalize.css (8.0.1-5) ... Setting up libdrm-common (2.4.124-2) ... Setting up libsnappy-jni (1.1.10.7-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:amd64 (2.6.9+dfsg-2) ... Setting up dbus-bin (1.16.2-2) ... Setting up liblsan0:amd64 (14.2.0-19) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libitm1:amd64 (14.2.0-19) ... 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 (1.7.0-2) ... Setting up libwayland-client0:amd64 (1.23.1-3) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.7-3) ... Setting up libwayland-server0:amd64 (1.23.1-3) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libnss3:amd64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libxom-java (1.3.9-1) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up libtbbbind-2-5:amd64 (2022.1.0-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.11+ds-5) ... Setting up libperl5.40:amd64 (5.40.1-2) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up perl (5.40.1-2) ... Setting up libglib2.0-0t64:amd64 (2.84.1-1) ... Setting up libmbedx509-7:amd64 (3.6.3-1) ... 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+b4) ... Setting up libjs-jquery-metadata (12-4) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up coinor-libosi1v5:amd64 (0.108.10+ds-2) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libmbedtls21:amd64 (3.6.3-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libdrm2:amd64 (2.4.124-2) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up libwayland-cursor0:amd64 (1.23.1-3) ... Setting up xml-core (0.19) ... Setting up libjson-perl (4.10000-1) ... Setting up libxslt1.1:amd64 (1.1.35-1.2) ... Setting up libpam-systemd:amd64 (257.5-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libc6-dev:amd64 (2.41-6) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libgcc-14-dev:amd64 (14.2.0-19) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libstdc++-14-dev:amd64 (14.2.0-19) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-1) ... Setting up libavahi-client3:amd64 (0.8-16) ... 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Setting up openjdk-21-jre-headless:amd64 (21.0.7~8ea-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 libtirpc3t64:amd64 (1.3.6+ds-1) ... Setting up python3.13 (3.13.3-1) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libpango-1.0-0:amd64 (1.56.3-1) ... Setting up libdrm-intel1:amd64 (2.4.124-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-2) ... Setting up python3 (3.13.3-1) ... Setting up libtbb12:amd64 (2022.1.0-1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-click (8.2.0+0.really.8.1.8-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up python3.13-tk (3.13.3-1) ... Setting up python3-plac (1.4.3-2) ... Setting up libcolord2:amd64 (1.4.7-3) ... Setting up python3-platformdirs (4.3.7-1) ... Setting up python3-psutil (7.0.0-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up python3-fs (2.4.16-7) ... Setting up liberror-perl (0.17030-1) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up dbus-user-session (1.16.2-2) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.2.1-1) ... Setting up python3-jinja2 (3.1.6-1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-xopen (1.7.0-3) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-humanfriendly (10.0-6) ... Setting up adwaita-icon-theme (48.0-1) ... 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 python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up coinor-libclp1:amd64 (1.17.10+ds-1) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libatspi2.0-0t64:amd64 (2.56.1-2) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up sphinx-common (8.1.3-5) ... 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 libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up python3-idna (3.10-1) ... Setting up python3-wrapt (1.15.0-4+b1) ... Setting up python3-markdown (3.7-2) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.13.1-1) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up python3-urllib3 (2.3.0-2) ... Setting up python3-markdown-it (3.0.0-2) ... Setting up python3-rpds-py (0.21.0-2+b1) ... Setting up python3-fastjsonschema (2.21.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up hisat2 (2.2.1-5+b3) ... Setting up python3-lxml:amd64 (5.3.2-1) ... Setting up python3-traitlets (5.14.3+really5.14.3-1) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-1+b1) ... Setting up python3-py2bit (0.3.3-1+b1) ... Setting up libcairo-gobject2:amd64 (1.18.4-1+b1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up coinor-libcgl1:amd64 (0.60.9+ds-1) ... Setting up python3-datrie:amd64 (0.8.2-5+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lzstring (1.0.4-3) ... Setting up python3-humanize (4.12.1-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up python3-smmap (6.0.0-1) ... Setting up libcups2t64:amd64 (2.4.10-2+b1) ... Setting up python3-jupyter-core (5.7.2-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... Setting up python3-dnaio (1.2.3-1+b1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-toposort (1.10-2) ... Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7.1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.56.1-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-configargparse (1.7-2) ... Setting up python3-sympy (1.13.3-5) ... Setting up python3-attr (25.3.0-1) ... Setting up mesa-libgallium:amd64 (25.0.3-1) ... Setting up libngs-jni:amd64 (3.0.9+dfsg-7.1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up python3-scipy (1.15.2-7) ... Setting up python3-importlib-metadata (8.6.1-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-smart-open (7.1.0-1) ... Setting up python3-py (1.11.0-4) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:amd64 (8.13.0-1) ... Setting up libgbm1:amd64 (25.0.3-1) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-deeptoolsintervals (0.1.9-3+b11) ... Setting up python3-rich (13.9.4-1) ... Setting up python3-lz4 (4.4.0+dfsg-2) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b4) ... Setting up blt (2.5.3+dfsg-8) ... Setting up python3-tenacity (8.4.2+really8.4.1-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up libgl1-mesa-dri:amd64 (25.0.3-1) ... Setting up libcurl3t64-gnutls:amd64 (8.13.0-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-yaml (6.0.2-1+b2) ... Setting up python3-tk:amd64 (3.13.3-1) ... Setting up python3-pytz (2025.2-1) ... Setting up dconf-service (0.40.0-5) ... Setting up python3-gitdb (4.0.12-1) ... Setting up python3-tz (2025.2-1) ... Setting up python3-yte (1.5.4-1) ... Setting up python3-pil:amd64 (11.1.0-5+b1) ... 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 python3-cutadapt (4.7-2+b3) ... Setting up python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Setting up python3-requests (2.32.3+dfsg-5) ... Setting up r-base-core (4.4.3-1+b1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.3-1) ... Setting up r-cran-squarem (2021.1-1) ... 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 python3-retry (0.9.2-3) ... Setting up git (1:2.49.0-1) ... Setting up r-cran-lattice (0.22-7-1) ... Setting up r-cran-nlme (3.1.168-1) ... 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 python3-rich-click (1.6.0-2) ... Setting up r-cran-zip (2.3.2-1) ... Setting up r-cran-xml (3.99-0.18-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-locfit (1.5-9.12-1) ... Setting up r-cran-sparsem (1.84-2-1+b1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up r-cran-nnet (7.3-20-1) ... Setting up libbigwig0t64:amd64 (0.4.7+dfsg-3.1+b2) ... 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 (1.9.5-1) ... Setting up r-cran-rjson (0.2.23-1) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up libngs-java:amd64 (3.0.9+dfsg-7.1) ... Setting up r-cran-r6 (2.6.1-1) ... 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 r-bioc-genomeinfodbdata (1.2.13-2) ... Setting up r-cran-microbenchmark (1.5.0-1) ... Setting up python3-referencing (0.36.2-1) ... Setting up r-cran-littler (0.3.21-1) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.5+dfsg-1) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-curl (6.2.1+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-cran-nloptr (2.2.1-2) ... Setting up r-cran-boot (1.3-31-1) ... Setting up r-cran-rematch (2.0.0-1) ... Setting up r-bioc-biocgenerics (0.52.0-2) ... Setting up r-cran-rlang (1.1.5-1) ... Setting up libglx-mesa0:amd64 (25.0.3-1) ... Setting up r-cran-matrixstats (1.5.0-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up r-cran-listenv (0.9.1+dfsg-1) ... Setting up littler (0.3.21-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up r-bioc-matrixgenerics (1.18.1-1) ... Setting up r-cran-xfun (0.51+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 cutadapt (4.7-2) ... 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 (1.0.2-1) ... Setting up r-cran-evaluate (1.0.3-1) ... 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 (1.0.6-1) ... Setting up r-cran-cardata (3.0.5-1) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up r-cran-mass (7.3-65-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-data.table (1.17.0+dfsg-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-foreign (0.8.90-1) ... Setting up r-cran-writexl (1.5.3-1) ... Setting up r-cran-bit (4.6.0+dfsg-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.4-1) ... Setting up r-cran-rbibutils (2.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bitops (1.0-9-1) ... Setting up r-cran-bit64 (4.6.0-1-1) ... Setting up r-cran-progressr (0.15.1-1) ... Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... Setting up samtools (1.21-1) ... 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 salmon (1.10.2+ds1-1+b5) ... Setting up r-cran-r.methodss3 (1.8.2-1) ... Setting up r-bioc-biobase (2.66.0-2) ... Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... Setting up r-cran-corrplot (0.95-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-parallelly (1.42.0-1) ... 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+b1) ... Setting up r-cran-cpp11 (0.5.2-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up python3-git (3.1.44-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-diagram (1.6.5-2) ... Setting up megadepth (1.2.0-4+b1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-later (1.4.1+dfsg-1) ... Setting up r-cran-matrix (1.7-3-1) ... Setting up r-cran-htmltools (0.5.8.1-1) ... 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:692: SyntaxWarning: invalid escape sequence '\s' :param sigma: Relative luminance parameter :math:`\sigma`. For average surround set :math:`\sigma=1/2.3`, /usr/lib/python3/dist-packages/colormath/color_appearance_models.py:798: SyntaxWarning: invalid escape sequence '\s' :param sigma: :math:`\sigma` /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+b3) ... Setting up r-cran-tinytex (0.56-1) ... Setting up r-bioc-tximport (1.34.0+dfsg-2) ... Setting up r-cran-kernsmooth (2.23-26-1) ... Setting up r-cran-knitr (1.50+dfsg-1) ... Setting up r-cran-mgcv (1.9-3-1) ... Setting up python3-stopit (1.1.2-3) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up r-cran-rcpparmadillo (14.4.1-1-1) ... Setting up r-bioc-iranges (2.40.1-2) ... Setting up r-cran-tzdb (0.5.0-1) ... Setting up r-cran-globals (0.16.3-1) ... Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... Setting up python3-jsonschema-specifications (2023.12.1-2) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up python3-htseq (2.0.9+dfsg-1+b2) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-minqa (1.2.8-1) ... Setting up r-cran-openssl (2.3.2+dfsg-1) ... Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-cran-class (7.3-23-1) ... Setting up r-bioc-biocparallel (1.40.0-2) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up python3-spectra (0.1.0-1) ... Setting up r-cran-openxlsx (4.2.8-1) ... Setting up trim-galore (0.6.10-1) ... Setting up python3-pulp (2.7.0+dfsg-4) ... /usr/lib/python3/dist-packages/pulp/apis/xpress_api.py:325: SyntaxWarning: invalid escape sequence '\ ' otherwise be interpreted by the Tcl shell: \ $ " [ Setting up r-cran-matrixmodels (0.5-4-1) ... Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ... Setting up r-cran-sparsevctrs (0.2.0-2) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up r-cran-clock (0.7.2-1) ... Setting up r-cran-proc (1.18.5-1) ... Setting up r-cran-fontawesome (0.5.3-1) ... Setting up r-cran-survival (3.8-3-1) ... Setting up r-bioc-biocio (1.16.0+dfsg-2) ... Setting up r-cran-r.oo (1.27.0-1) ... Setting up r-cran-rdpack (2.6.3-1) ... 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-tidyselect (1.2.1+dfsg-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-cran-future.apply (1.11.3+dfsg-1) ... Setting up r-cran-timechange (0.3.0-1) ... Setting up python3-jsonschema (4.19.2-6) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up libgtk-3-0t64:amd64 (3.24.49-3) ... 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 (1.8.1+dfsg-1) ... Setting up r-cran-promises (1.3.2+dfsg-1) ... Setting up r-cran-purrr (1.0.4-1) ... Setting up r-cran-e1071 (1.7-16-1) ... Setting up r-bioc-xvector (0.46.0-2) ... Setting up r-cran-hardhat (1.4.1+dfsg-1) ... Setting up r-cran-dplyr (1.1.4-4) ... Setting up r-cran-reformulas (0.4.0-2) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-lubridate (1.9.4+dfsg-1) ... Setting up r-cran-r.utils (2.13.0-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-cran-prodlim (2024.06.25-1) ... Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ... 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 (4.1.24-1) ... Setting up r-cran-ggsci (3.2.0-1) ... Setting up python3-nbformat (5.9.1-1) ... Setting up r-cran-ipred (0.9-15-1) ... Setting up r-cran-lme4 (1.1-37-1) ... Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... Setting up r-cran-bslib (0.9.0+dfsg-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up r-cran-ggrepel (0.9.6-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up python3-plotly (5.20.0+dfsg-1) ... Setting up r-cran-recipes (1.1.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ... Setting up r-cran-cowplot (1.1.3+dfsg-1) ... Setting up r-cran-readxl (1.4.5-1) ... Setting up r-cran-haven (2.5.4-1) ... Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... Setting up r-cran-caret (7.0-1+dfsg-1) ... Setting up r-cran-shiny (1.10.0+dfsg-2) ... Setting up r-cran-shinyjs (2.1.0-1) ... Setting up r-cran-miniui (0.1.1.1-3) ... Setting up r-cran-broom (1.0.7+dfsg-1) ... Setting up r-cran-rmarkdown (2.29+dfsg-1) ... Setting up r-cran-conquer (1.3.3-1) ... Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... Setting up r-cran-crosstalk (1.2.1+dfsg-1) ... Setting up r-cran-rio (1.2.3-1) ... Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... Setting up r-cran-quantreg (6.1-1) ... Setting up r-bioc-deseq2 (1.46.0+dfsg-2) ... 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 r-cran-doby (4.6.25-1) ... Setting up r-bioc-genomicalignments (1.42.0-2) ... Setting up r-bioc-rtracklayer (1.66.0-2) ... Setting up r-cran-dt (0.33+dfsg-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 (4.57.0-1) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-2) ... Setting up multiqc (1.21+dfsg-2) ... Processing triggers for libc-bin (2.41-6) ... Processing triggers for systemd (257.5-2) ... Processing triggers for procps (2:4.0.4-7) ... 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:FIRMAPROFESIONAL_CA_ROOT-A_WEB.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:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.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: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_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.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 junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up openjdk-21-jre:amd64 (21.0.7~8ea-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... 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 (7.32.4-7) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-numpydoc (1.8.0-1) ... Setting up python3-deeptools (3.5.6+dfsg-1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20241223) ... 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. 1m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 1m10.6s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 1m10.6s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmps0rc_fks/./tmp/piuparts-depends-dummy.deb 1m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 1m10.6s DUMP: piuparts-depends-dummy install ok installed 1m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 1m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', 'piuparts-depends-dummy'] 1m10.6s DUMP: (Reading database ... 99088 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 1m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', 'piuparts-depends-dummy'] 1m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 1m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 1m10.7s DEBUG: Recording chroot state 1m11.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 1m15.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 1m20.9s ERROR: WARN: Broken symlinks: /etc/vconsole.conf -> default/keyboard /etc/default/locale -> ../locale.conf /usr/lib/jvm/java-21-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so 1m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m21.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m21.4s DUMP: pigx-rnaseq: Installed: (none) Candidate: 0.1.1-1 Version table: 0.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 1m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 1m22.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: rna-star The following NEW packages will be installed: pigx-rnaseq 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 61.7 kB of archives. After this operation, 180 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 pigx-rnaseq all 0.1.1-1 [61.7 kB] Fetched 61.7 kB in 0s (407 kB/s) Selecting previously unselected package pigx-rnaseq. (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 ... 99088 files and directories currently installed.) Preparing to unpack .../pigx-rnaseq_0.1.1-1_all.deb ... Unpacking pigx-rnaseq (0.1.1-1) ... Setting up pigx-rnaseq (0.1.1-1) ... 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 1m22.1s INFO: Running scripts post_install 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'systemd-tmpfiles', '--cat-config'] 1m22.1s DUMP: # /usr/lib/tmpfiles.d/20-systemd-shell-extra.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. L$ /etc/profile.d/70-systemd-shell-extra.sh - - - - /usr/lib/systemd/profile.d/70-systemd-shell-extra.sh # /usr/lib/tmpfiles.d/20-systemd-ssh-generator.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. L$ /etc/ssh/ssh_config.d/20-systemd-ssh-proxy.conf - - - - /usr/lib/systemd/ssh_config.d/20-systemd-ssh-proxy.conf d /run/sshd 0755 # /usr/lib/tmpfiles.d/20-systemd-stub.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Copy systemd-stub provided metadata such as PCR signature and public key file # from initrd into /run/, so that it will survive the initrd stage C /run/systemd/stub/profile 0444 root root - /.extra/profile C /run/systemd/stub/os-release 0444 root root - /.extra/os-release C /run/systemd/tpm2-pcr-signature.json 0444 root root - /.extra/tpm2-pcr-signature.json C /run/systemd/tpm2-pcr-public-key.pem 0444 root root - /.extra/tpm2-pcr-public-key.pem # /usr/lib/tmpfiles.d/credstore.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d /etc/credstore 0700 root root d /etc/credstore.encrypted 0700 root root z /run/credstore 0700 root root z /run/credstore.encrypted 0700 root root # /usr/lib/tmpfiles.d/dbus.conf # Fields: type; path; mode; uid; gid; age; argument (symlink target) # Make ${localstatedir}/lib/dbus (required for systemd < 237) # Adjust mode and ownership if it already exists. d /var/lib/dbus 0755 - - - # Make ${localstatedir}/lib/dbus/machine-id a symlink to /etc/machine-id # if it does not already exist L /var/lib/dbus/machine-id - - - - /etc/machine-id # /usr/lib/tmpfiles.d/debian.conf # This file is part of the debianisation of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details # Type Path Mode UID GID Age Argument L /run/shm - - - - /dev/shm d /run/sendsigs.omit.d 0755 root root - d /run/lock 1777 root root - - L+ /etc/mtab - - - - ../proc/self/mounts L+ /etc/default/locale - - - - ../locale.conf L+ /etc/vconsole.conf - - - - default/keyboard # /usr/lib/tmpfiles.d/home.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. Q /home 0755 - - - q /srv 0755 - - - # /usr/lib/tmpfiles.d/journal-nocow.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Set the NOCOW attribute for directories of journal files. This flag # is inherited by their new files and sub-directories. Matters only # for btrfs filesystems. # # WARNING: Enabling the NOCOW attribute improves journal performance # substantially, but also disables the btrfs checksum logic. In # btrfs RAID filesystems the checksums are needed for rebuilding # corrupted files. Without checksums such rebuilds are not # possible. # # In a single-disk filesystem (or a filesystem without redundancy) # enabling the NOCOW attribute for journal files is safe, because # they have their own checksums and a rebuilding wouldn't be possible # in any case. h /var/log/journal - - - - +C h /var/log/journal/%m - - - - +C h /var/log/journal/remote - - - - +C # /usr/lib/tmpfiles.d/legacy.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # The functionality provided by these files and directories has been replaced # by newer interfaces. Their use is discouraged on legacy-free systems. This # configuration is provided to maintain backward compatibility. d /run/lock 0755 root root - L /var/lock - - - - ../run/lock L$ /var/log/README - - - - ../../usr/share/doc/systemd/README.logs # /run/lock/subsys is used for serializing SysV service execution, and # hence without use on SysV-less systems. d /run/lock/subsys 0755 root root - # /forcefsck, /fastboot and /forcequotacheck are deprecated in favor of the # kernel command line options 'fsck.mode=force', 'fsck.mode=skip' and # 'quotacheck.mode=force' r! /forcefsck r! /fastboot r! /forcequotacheck # /usr/lib/tmpfiles.d/libselinux1.conf # See tmpfiles.d(5) for details # Type Path Mode UID GID Age Argument d /run/setrans 0755 root root - - # /usr/lib/tmpfiles.d/passwd.conf # If a password operation is in progress and we lose power, stale lockfiles # can be left behind. Clear them on boot. r! /etc/gshadow.lock r! /etc/shadow.lock r! /etc/passwd.lock r! /etc/group.lock r! /etc/subuid.lock r! /etc/subgid.lock # /usr/lib/tmpfiles.d/provision.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Provision additional login messages from credentials, if they are set. Note # that these lines are NOPs if the credentials are not set or if the files # already exist. f^ /etc/motd.d/50-provision.conf - - - - login.motd f^ /etc/issue.d/50-provision.conf - - - - login.issue # Provision a /etc/hosts file from credentials. f^ /etc/hosts - - - - network.hosts # Provision SSH key for root d- /root :0700 root :root - d- /root/.ssh :0700 root :root - f^ /root/.ssh/authorized_keys :0600 root :root - ssh.authorized_keys.root # /usr/lib/tmpfiles.d/systemd-network.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d$ /run/systemd/netif 0755 systemd-network systemd-network - d$ /run/systemd/netif/links 0755 systemd-network systemd-network - d$ /run/systemd/netif/leases 0755 systemd-network systemd-network - d$ /var/lib/systemd/network 0755 systemd-network systemd-network - # /usr/lib/tmpfiles.d/systemd-nologin.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5), systemd-user-sessions.service(8) and pam_nologin(8). f+! /run/nologin 0644 - - - "System is booting up. Unprivileged users are not permitted to log in yet. Please come back later. For technical details, see pam_nologin(8)." # /usr/lib/tmpfiles.d/systemd-pstore.conf # SPDX-License-Identifier: LGPL-2.1-or-later # # The systemd-pstore.service(1) archives the contents of /sys/fs/pstore # upon boot so that there is room for a subsequent dump. This service # is enabled with: # systemctl enable systemd-pstore # # With the service enabled, the kernel still needs to be configured # to write data into the pstore. The kernel has two parameters, # crash_kexec_post_notifiers and printk.always_kmsg_dump, that # control writes into pstore. # # The crash_kexec_post_notifiers parameter enables the kernel to write # dmesg (including stack trace) into pstore upon a panic even if kdump # is loaded, only needed if you want to use pstore with kdump. Without # this parameter, kdump could block writing to pstore for stability # reason. Note this increases the risk of kdump failure even if pstore # is not available. # # The printk.always_kmsg_dump parameter enables the kernel to write dmesg # upon a normal shutdown (shutdown, reboot, halt). # # To configure the kernel parameters, uncomment the appropriate # lines below. The value written is either 'Y' to enable the # kernel parameter, or 'N' to disable the kernel parameter. # # After making a change to this file, do: # systemd-tmpfiles --create path/to/tmpfiles.d/systemd-pstore.conf # # These changes are automatically applied on future re-boots. d /var/lib/systemd/pstore 0755 root root 14d #w- /sys/module/printk/parameters/always_kmsg_dump - - - - Y #w- /sys/module/kernel/parameters/crash_kexec_post_notifiers - - - - Y # /usr/lib/tmpfiles.d/systemd-tmp.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Exclude namespace mountpoints created with PrivateTmp=yes x /tmp/systemd-private-%b-* X /tmp/systemd-private-%b-*/tmp x /var/tmp/systemd-private-%b-* X /var/tmp/systemd-private-%b-*/tmp # Remove top-level private temporary directories on each boot R! /tmp/systemd-private-* R! /var/tmp/systemd-private-* # Handle lost systemd-coredump temp files. They could be lost on old filesystems, # for example, after hard reboot. x /var/lib/systemd/coredump/.#core*.%b* r! /var/lib/systemd/coredump/.#* # /usr/lib/tmpfiles.d/systemd.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. d /run/user 0755 root root - d /run/systemd/ask-password 0755 root root - d$ /run/systemd/seats 0755 root root - d$ /run/systemd/sessions 0755 root root - d$ /run/systemd/users 0755 root root - d /run/systemd/machines 0755 root root - d$ /run/systemd/shutdown 0755 root root - d /run/log 0755 root root - z /run/log/journal 2755 root systemd-journal - - Z /run/log/journal/%m ~2750 root systemd-journal - - a+ /run/log/journal - - - - d:group::r-x,d:group:adm:r-x,group::r-x,group:adm:r-x A+ /run/log/journal/%m - - - - d:group:adm:r-x,group:adm:r-X z /var/log/journal 2755 root systemd-journal - - z /var/log/journal/%m 2755 root systemd-journal - - z /var/log/journal/%m/system.journal 0640 root systemd-journal - - a+ /var/log/journal - - - - d:group::r-x,d:group:adm:r-x,group::r-x,group:adm:r-x a+ /var/log/journal/%m - - - - d:group:adm:r-x,group:adm:r-x a+ /var/log/journal/%m/system.journal - - - - group:adm:r-- d /var/lib/systemd 0755 root root - d /var/lib/systemd/coredump 0755 root root 2w # Files and directories in /var/lib/systemd/ephemeral-trees are locked by pid 1 to prevent tmpfiles from # removing them, and tmpfiles is told to clean up anything in /var/lib/systemd/ephemeral-trees that isn't # locked unconditionally. d /var/lib/systemd/ephemeral-trees 0755 root root 0 d /var/lib/private 0700 root root - d /var/log/private 0700 root root - d /var/cache/private 0700 root root - # /usr/lib/tmpfiles.d/tmp.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Clear tmp directories separately, to make them easier to override q /tmp 1777 root root 10d q /var/tmp 1777 root root 30d # /usr/lib/tmpfiles.d/var.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. q /var 0755 - - - L /var/run - - - - ../run d /var/log 0755 - - - d /var/cache 0755 - - - d /var/lib 0755 - - - d /var/spool 0755 - - - # /usr/lib/tmpfiles.d/x11.conf # This file is part of systemd. # # systemd is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by # the Free Software Foundation; either version 2.1 of the License, or # (at your option) any later version. # See tmpfiles.d(5) for details. # Make sure these are created by default so that nobody else can # or empty them at startup D! /tmp/.X11-unix 1777 root root 10d D! /tmp/.ICE-unix 1777 root root 10d D! /tmp/.XIM-unix 1777 root root 10d D! /tmp/.font-unix 1777 root root 10d # Unlink the X11 lock files r! /tmp/.X[0-9]*-lock 1m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'systemd-tmpfiles', '--cat-config'] 1m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'remove', 'pigx-rnaseq'] 1m22.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: adwaita-icon-theme at-spi2-common blt ca-certificates-java coinor-cbc coinor-libcbc3.1 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cutadapt 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 junit4 libapache-pom-java 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 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm2 libedit2 libepoxy0 liberror-perl libezmorph-java libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu76 libimagequant0 libisal2 libitm1 libjaxen-java 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-java libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnspr4 libnss3 libnuma1 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libtasn1-6 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-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 libzopfli1 linux-libc-dev littler media-types megadepth mesa-libgallium multiqc ncbi-vdb-data node-bootstrap-sass node-html5shiv node-normalize.css openjdk-21-jre openjdk-21-jre-headless pandoc pandoc-data pigz python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click 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-numpy-dev 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-pytz python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy 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-zopfli python3.13 python3.13-minimal 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-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 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-sparsevctrs 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 sgml-base shared-mime-info snakemake sphinx-common tk8.6-blt2.5 trim-galore unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: pigx-rnaseq 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 180 kB 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 ... 99115 files and directories currently installed.) Removing pigx-rnaseq (0.1.1-1) ... 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'remove', 'pigx-rnaseq'] 1m22.6s INFO: Reinstalling after remove 1m22.6s INFO: Running scripts pre_install 1m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 1m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m22.7s 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: 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m22.7s DUMP: pigx-rnaseq: Installed: (none) Candidate: 0.1.1-1 Version table: 0.1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 1m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 1m23.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Recommended packages: rna-star The following NEW packages will be installed: pigx-rnaseq 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/61.7 kB of archives. After this operation, 180 kB of additional disk space will be used. Selecting previously unselected package pigx-rnaseq. (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 ... 99088 files and directories currently installed.) Preparing to unpack .../pigx-rnaseq_0.1.1-1_all.deb ... Unpacking pigx-rnaseq (0.1.1-1) ... Setting up pigx-rnaseq (0.1.1-1) ... 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.1-1'] 1m23.3s INFO: Running scripts post_install 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m23.3s INFO: Running scripts pre_install 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_database-server'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_exceptions'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_extras'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m23.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy'] 1m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m23.4s 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 1m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-cache', 'policy', 'pigx-rnaseq'] 1m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', '--reinstall', 'pigx-rnaseq=0.1.1-1'] 1m23.9s DUMP: Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/61.7 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 99115 files and directories currently installed.) Preparing to unpack .../pigx-rnaseq_0.1.1-1_all.deb ... Unpacking pigx-rnaseq (0.1.1-1) over (0.1.1-1) ... Setting up pigx-rnaseq (0.1.1-1) ... 1m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', '-y', 'install', '--reinstall', 'pigx-rnaseq=0.1.1-1'] 1m23.9s INFO: Running scripts post_install 1m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_install_exceptions'] 1m24.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 1m27.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 1m27.3s INFO: IGNORED broken symlink: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 1m27.3s INFO: IGNORED broken symlink: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 1m33.1s ERROR: WARN: Broken symlinks: /usr/lib/jvm/java-21-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so (openjdk-21-jre:amd64) 1m37.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', '-ac', '--ignore-obsolete'] 1m43.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', '-ac', '--ignore-obsolete'] 1m43.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m43.3s DUMP: 0.15.6 1m43.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m43.3s INFO: Running adequate version 0.15.6 now. 1m43.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'pigx-rnaseq'] 1m43.4s 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 1m43.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'pigx-rnaseq'] 1m43.4s 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 1m43.4s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 1m43.4s INFO: Running scripts pre_remove 1m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m43.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m43.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m52.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m52.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_exceptions'] 1m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_exceptions'] 1m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_preseed_cleanup'] 1m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/pre_remove_preseed_cleanup'] 1m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m53.2s DUMP: install ok installed adwaita-icon-theme adwaita-icon-theme 48.0-1 install ok installed apt apt 3.0.0 install ok installed at-spi2-common at-spi2-common 2.56.1-2 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed blt blt 2.5.3+dfsg-8 install ok installed bsdutils bsdutils 1:2.41-3 install ok installed ca-certificates ca-certificates 20241223 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-5 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.10+ds-2 install ok installed coreutils coreutils 9.7-1 install ok installed cutadapt cutadapt 4.7-2 install ok installed dash dash 0.5.12-12 install ok installed dbconfig-common dbconfig-common 2.0.24 install ok installed dbus dbus 1.16.2-2 install ok installed dbus-bin dbus-bin 1.16.2-2 install ok installed dbus-daemon dbus-daemon 1.16.2-2 install ok installed dbus-session-bus-common dbus-session-bus-common 1.16.2-2 install ok installed dbus-system-bus-common dbus-system-bus-common 1.16.2-2 install ok installed dbus-user-session dbus-user-session 1.16.2-2 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-5 install ok installed dconf-service dconf-service 0.40.0-5 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 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 1:3.10-3 install ok installed docutils-common docutils-common 0.21.2+dfsg-2 install ok installed dpkg dpkg 1.22.18 install ok installed fastp fastp 0.24.0+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 2.15.0-2.3 install ok installed fontconfig-config fontconfig-config 2.15.0-2.3 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 2.4.3-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed git git 1:2.49.0-1 install ok installed git-man git-man 1:2.49.0-1 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 4.18.4+ds-1 install ok installed gzip gzip 1.13-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-2 install ok installed hisat2 hisat2 2.2.1-5+b3 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed java-common java-common 0.76 install ok installed javascript-common javascript-common 12 install ok installed junit4 junit4 4.13.2-5 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 4.1.0~beta5-6 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libasan8:amd64 libasan8 14.2.0-19 install ok installed libasound2-data libasound2-data 1.2.13-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.13-1+b1 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.56.1-2 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.56.1-2 install ok installed libatomic1:amd64 libatomic1 14.2.0-19 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.56.1-2 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-16 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-16 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-16 install ok installed libbigwig0t64:amd64 libbigwig0t64 0.4.7+dfsg-3.1+b2 install ok installed libblas3:amd64 libblas3 3.12.1-2 install ok installed libblkid1:amd64 libblkid1 2.41-3 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 1.83.0-4.2 install ok installed libboost-iostreams1.83.0:amd64 libboost-iostreams1.83.0 1.83.0-4.2 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-4.2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-4.2 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 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 2.41-6 install ok installed libc-dev-bin libc-dev-bin 2.41-6 install ok installed libc6:amd64 libc6 2.41-6 install ok installed libc6-dev:amd64 libc6-dev 2.41-6 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.4-1+b1 install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-4 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-2 install ok installed libcolord2:amd64 libcolord2 1.4.7-3 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1 install ok installed libcommons-beanutils-java libcommons-beanutils-java 1.9.4-2 install ok installed libcommons-codec-java libcommons-codec-java 1.18.0-1 install ok installed libcommons-collections3-java libcommons-collections3-java 3.2.2-3 install ok installed libcommons-collections4-java libcommons-collections4-java 4.4-2 install ok installed libcommons-compress-java libcommons-compress-java 1.27.1-2 install ok installed libcommons-io-java libcommons-io-java 2.18.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.17.0-1 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-1 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-4 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.38-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-2+b1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.13.0-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.13.0-1 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 1.16.2-2 install ok installed libdconf1:amd64 libdconf1 0.40.0-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.124-2 install ok installed libdrm-common libdrm-common 2.4.124-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.124-2 install ok installed libdrm2:amd64 libdrm2 2.4.124-2 install ok installed libedit2:amd64 libedit2 3.1-20250104-1 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 0.17030-1 install ok installed libexpat1:amd64 libexpat1 2.7.1-1 install ok installed libezmorph-java libezmorph-java 1.0.6-4 install ok installed libffi8:amd64 libffi8 3.4.7-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgbm1:amd64 libgbm1 25.0.3-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-19 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7 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-2 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 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 25.0.3-1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b2 install ok installed libglx-mesa0:amd64 libglx-mesa0 25.0.3-1 install ok installed libglx0:amd64 libglx0 1.7.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-19 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.49-3 install ok installed libgtk-3-common libgtk-3-common 3.24.49-3 install ok installed libhamcrest-java libhamcrest-java 2.2-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libhtsjdk-java libhtsjdk-java 4.1.3+dfsg-2 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-19 install ok installed libhwloc15:amd64 libhwloc15 2.12.0-1 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu76:amd64 libicu76 76.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libisal2 libisal2 2.31.1-1.1 install ok installed libitm1:amd64 libitm1 14.2.0-19 install ok installed libjaxen-java libjaxen-java 1.1.6-5 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 5.3.0-3 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1 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 8.1.3-5 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-java libjson-java 3.1.0+dfsg-2 install ok installed libjson-perl libjson-perl 4.10000-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-5 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblapack3:amd64 liblapack3 3.12.1-2 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed libllvm19:amd64 libllvm19 1:19.1.7-3 install ok installed liblsan0:amd64 liblsan0 14.2.0-19 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.7-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.3-1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.3-1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.3-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-3 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.9+dfsg-7.1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.9+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.5+20250216-2 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.9+dfsg-7.1 install ok installed libngs-jni:amd64 libngs-jni 3.0.9+dfsg-7.1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libnlopt0:amd64 libnlopt0 2.7.1-6+b4 install ok installed libnspr4:amd64 libnspr4 2:4.36-1 install ok installed libnss3:amd64 libnss3 2:3.110-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.3-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam-systemd:amd64 libpam-systemd 257.5-2 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.56.3-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.56.3-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.56.3-1 install ok installed libpaper-utils libpaper-utils 2.2.5-0.3+b2 install ok installed libpaper2:amd64 libpaper2 2.2.5-0.3+b2 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.3-1 install ok installed libperl5.40:amd64 libperl5.40 5.40.1-2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.3-1 install ok installed libpython3.13:amd64 libpython3.13 3.13.3-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.3-1 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.3-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-19 install ok installed libraqm0:amd64 libraqm0 0.10.2-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 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+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 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 3.8.1-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libslf4j-java libslf4j-java 1.7.32-1 install ok installed libsm6:amd64 libsm6 2:1.2.6-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3 install ok installed libsnappy-java libsnappy-java 1.1.10.7-1 install ok installed libsnappy-jni libsnappy-jni 1.1.10.7-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.2.2-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstaden-read14t64:amd64 libstaden-read14t64 1.15.0-1.1+b2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-19 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd-shared:amd64 libsystemd-shared 257.5-2 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtbb12:amd64 libtbb12 2022.1.0-1 install ok installed libtbbbind-2-5:amd64 libtbbbind-2-5 2022.1.0-1 install ok installed libtbbmalloc2:amd64 libtbbmalloc2 2022.1.0-1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 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 4.7.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libtirpc-common libtirpc-common 1.3.6+ds-1 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.6+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-19 install ok installed libubsan1:amd64 libubsan1 14.2.0-19 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-3 install ok installed libuv1t64:amd64 libuv1t64 1.50.0-2 install ok installed libvulkan1:amd64 libvulkan1 1.4.309.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.1-3 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.1-3 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.1-3 install ok installed libwayland-server0:amd64 libwayland-server0 1.23.1-3 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.5.0-0.1 install ok installed libwebpmux3:amd64 libwebpmux3 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 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 1:1.2.3-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxerces2-java libxerces2-java 2.12.2-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b4 install ok installed libxft2:amd64 libxft2 2.3.6-1+b4 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b4 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.7.0-2 install ok installed libxml-commons-external-java libxml-commons-external-java 1.4.01-6 install ok installed libxml-commons-resolver1.1-java libxml-commons-resolver1.1-java 1.2-11 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4 install ok installed libxom-java libxom-java 1.3.9-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1+b3 install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3.3-1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.2 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b2 install ok installed libxtst6:amd64 libxtst6 2:1.2.5-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzopfli1 libzopfli1 1.0.3-3 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed linux-libc-dev linux-libc-dev 6.12.21-1 install ok installed littler littler 0.3.21-1 install ok installed login login 1:4.16.0-2+really2.41-3 install ok installed login.defs login.defs 1:4.17.4-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed media-types media-types 13.0.0 install ok installed megadepth megadepth 1.2.0-4+b1 install ok installed mesa-libgallium:amd64 mesa-libgallium 25.0.3-1 install ok installed mount mount 2.41-3 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+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed netbase netbase 6.5 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 21.0.7~8ea-1 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.7~8ea-1 install ok installed openssl openssl 3.5.0-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 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 1:4.17.4-1 install ok installed perl perl 5.40.1-2 install ok installed perl-base perl-base 5.40.1-2 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.1-2 install ok installed pigx-rnaseq pigx-rnaseq 0.1.1-1 install ok installed pigz pigz 2.8-1 install ok installed procps procps 2:4.0.4-7 install ok installed python-babel-localedata python-babel-localedata 2.17.0-1 install ok installed python-matplotlib-data python-matplotlib-data 3.10.1+dfsg1-2 install ok installed python3 python3 3.13.3-1 install ok installed python3-alabaster python3-alabaster 0.7.16-0.1 install ok installed python3-attr python3-attr 25.3.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-babel python3-babel 2.17.0-1 install ok installed python3-brotli python3-brotli 1.1.0-2+b7 install ok installed python3-certifi python3-certifi 2025.1.31+ds-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.1-1+b1 install ok installed python3-click python3-click 8.2.0+0.really.8.1.8-1 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 1.7-2 install ok installed python3-connection-pool python3-connection-pool 0.0.3-2 install ok installed python3-contourpy python3-contourpy 1.3.1-1+b1 install ok installed python3-cutadapt python3-cutadapt 4.7-2+b3 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-4 install ok installed python3-datrie:amd64 python3-datrie 0.8.2-5+b2 install ok installed python3-decorator python3-decorator 5.2.1-1 install ok installed python3-deeptools python3-deeptools 3.5.6+dfsg-1 install ok installed python3-deeptoolsintervals python3-deeptoolsintervals 0.1.9-3+b11 install ok installed python3-defusedxml python3-defusedxml 0.7.1-3 install ok installed python3-dnaio python3-dnaio 1.2.3-1+b1 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 2.21.1-1 install ok installed python3-fonttools python3-fonttools 4.57.0-1 install ok installed python3-fs python3-fs 2.4.16-7 install ok installed python3-git python3-git 3.1.44-1 install ok installed python3-gitdb python3-gitdb 4.0.12-1 install ok installed python3-htseq python3-htseq 2.0.9+dfsg-1+b2 install ok installed python3-humanfriendly python3-humanfriendly 10.0-6 install ok installed python3-humanize python3-humanize 4.12.1-1 install ok installed python3-idna python3-idna 3.10-1 install ok installed python3-imagesize python3-imagesize 1.4.1-1 install ok installed python3-importlib-metadata python3-importlib-metadata 8.6.1-1 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.1-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-jinja2 python3-jinja2 3.1.6-1 install ok installed python3-jsonschema python3-jsonschema 4.19.2-6 install ok installed python3-jsonschema-specifications python3-jsonschema-specifications 2023.12.1-2 install ok installed python3-jupyter-core python3-jupyter-core 5.7.2-5 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-3+b1 install ok installed python3-lxml:amd64 python3-lxml 5.3.2-1 install ok installed python3-lz4 python3-lz4 4.4.0+dfsg-2 install ok installed python3-lzstring python3-lzstring 1.0.4-3 install ok installed python3-markdown python3-markdown 3.7-2 install ok installed python3-markdown-it python3-markdown-it 3.0.0-2 install ok installed python3-markupsafe python3-markupsafe 2.1.5-1+b3 install ok installed python3-matplotlib python3-matplotlib 3.10.1+dfsg1-2 install ok installed python3-mdurl python3-mdurl 0.1.2-1 install ok installed python3-minimal python3-minimal 3.13.3-1 install ok installed python3-more-itertools python3-more-itertools 10.6.0-1 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 3.2.1-5 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-numpydoc python3-numpydoc 1.8.0-1 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pil:amd64 python3-pil 11.1.0-5+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 11.1.0-5+b1 install ok installed python3-pkg-resources python3-pkg-resources 75.8.0-1 install ok installed python3-plac python3-plac 1.4.3-2 install ok installed python3-platformdirs python3-platformdirs 4.3.7-1 install ok installed python3-plotly python3-plotly 5.20.0+dfsg-1 install ok installed python3-psutil python3-psutil 7.0.0-1 install ok installed python3-pulp python3-pulp 2.7.0+dfsg-4 install ok installed python3-py python3-py 1.11.0-4 install ok installed python3-py2bit python3-py2bit 0.3.3-1+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+b3 install ok installed python3-pygments python3-pygments 2.18.0+dfsg-2 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1 install ok installed python3-pytz python3-pytz 2025.2-1 install ok installed python3-ratelimiter python3-ratelimiter 1.2.0.post0-4 install ok installed python3-referencing python3-referencing 0.36.2-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-5 install ok installed python3-retry python3-retry 0.9.2-3 install ok installed python3-rich python3-rich 13.9.4-1 install ok installed python3-rich-click python3-rich-click 1.6.0-2 install ok installed python3-roman python3-roman 5.0-1 install ok installed python3-rpds-py python3-rpds-py 0.21.0-2+b1 install ok installed python3-scipy python3-scipy 1.15.2-7 install ok installed python3-smart-open python3-smart-open 7.1.0-1 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 0.1.0-1 install ok installed python3-sphinx python3-sphinx 8.1.3-5 install ok installed python3-stopit python3-stopit 1.1.2-3 install ok installed python3-sympy python3-sympy 1.13.3-5 install ok installed python3-tabulate python3-tabulate 0.9.0-1 install ok installed python3-tenacity python3-tenacity 8.4.2+really8.4.1-2 install ok installed python3-throttler python3-throttler 1.2.2-2 install ok installed python3-tk:amd64 python3-tk 3.13.3-1 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 4.4.2-1 install ok installed python3-typing-extensions python3-typing-extensions 4.13.1-1 install ok installed python3-tz python3-tz 2025.2-1 install ok installed python3-ufolib2 python3-ufolib2 0.17.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b4 install ok installed python3-urllib3 python3-urllib3 2.3.0-2 install ok installed python3-wrapt python3-wrapt 1.15.0-4+b1 install ok installed python3-xopen python3-xopen 1.7.0-3 install ok installed python3-yaml python3-yaml 6.0.2-1+b2 install ok installed python3-yte python3-yte 1.5.4-1 install ok installed python3-zipp python3-zipp 3.21.0-1 install ok installed python3-zopfli python3-zopfli 0.2.3.post1-1+b1 install ok installed python3.13 python3.13 3.13.3-1 install ok installed python3.13-minimal python3.13-minimal 3.13.3-1 install ok installed python3.13-tk python3.13-tk 3.13.3-1 install ok installed r-base-core r-base-core 4.4.3-1+b1 install ok installed r-bioc-biobase r-bioc-biobase 2.66.0-2 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.52.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.16.0+dfsg-2 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.40.0-2 install ok installed r-bioc-biostrings r-bioc-biostrings 2.74.1+dfsg-2 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.32.0+dfsg-2 install ok installed r-bioc-deseq2 r-bioc-deseq2 1.46.0+dfsg-2 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.42.3+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.13-2 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.42.0-2 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.58.0+dfsg-2 install ok installed r-bioc-iranges r-bioc-iranges 2.40.1-2 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.18.1-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 3.2.0+dfsg-2 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.22.0+dfsg-2 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.66.0-2 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.6.0+dfsg-2 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.44.0+dfsg-2 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.6.2+dfsg-2 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.36.0+dfsg-2 install ok installed r-bioc-tximport r-bioc-tximport 1.34.0+dfsg-2 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.2.0+ds-2 install ok installed r-bioc-xvector r-bioc-xvector 0.46.0-2 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.52.0+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 4.6.0+dfsg-1 install ok installed r-cran-bit64 r-cran-bit64 4.6.0-1-1 install ok installed r-cran-bitops r-cran-bitops 1.0-9-1 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 0.9.0+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 7.0-1+dfsg-1 install ok installed r-cran-cellranger r-cran-cellranger 1.1.0-3 install ok installed r-cran-class r-cran-class 7.3-23-1 install ok installed r-cran-cli r-cran-cli 3.6.4-1 install ok installed r-cran-clipr r-cran-clipr 0.8.0-1 install ok installed r-cran-clock r-cran-clock 0.7.2-1 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 1.9.5-1 install ok installed r-cran-conquer r-cran-conquer 1.3.3-1 install ok installed r-cran-corrplot r-cran-corrplot 0.95-1 install ok installed r-cran-cowplot r-cran-cowplot 1.1.3+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.5.2-1 install ok installed r-cran-crayon r-cran-crayon 1.5.3-1 install ok installed r-cran-crosstalk r-cran-crosstalk 1.2.1+dfsg-1 install ok installed r-cran-curl r-cran-curl 6.2.1+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.17.0+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 4.6.25-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-4 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 1.0.3-1 install ok installed r-cran-fansi r-cran-fansi 1.0.6-1 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 0.5.3-1 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 0.8.90-1 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 1.6.5+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 1.11.3+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 0.9.6-1 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 1.8.0-1 install ok installed r-cran-gower r-cran-gower 1.0.2-1 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 1.4.1+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 1.9.1+dfsg-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-26-1 install ok installed r-cran-knitr r-cran-knitr 1.50+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 1.4.1+dfsg-1 install ok installed r-cran-lattice r-cran-lattice 0.22-7-1 install ok installed r-cran-lava r-cran-lava 1.8.1+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 0.3.21-1 install ok installed r-cran-lme4 r-cran-lme4 1.1-37-1 install ok installed r-cran-locfit r-cran-locfit 1.5-9.12-1 install ok installed r-cran-lubridate r-cran-lubridate 1.9.4+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-65-1 install ok installed r-cran-matrix r-cran-matrix 1.7-3-1 install ok installed r-cran-matrixmodels r-cran-matrixmodels 0.5-4-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.5.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-3-1 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 3.1.168-1 install ok installed r-cran-nloptr r-cran-nloptr 2.2.1-2 install ok installed r-cran-nnet r-cran-nnet 7.3-20-1 install ok installed r-cran-numderiv r-cran-numderiv 2016.8-1.1-3 install ok installed r-cran-openssl r-cran-openssl 2.3.2+dfsg-1 install ok installed r-cran-openxlsx r-cran-openxlsx 4.2.8-1 install ok installed r-cran-parallelly r-cran-parallelly 1.42.0-1 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 1.10.1+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 0.15.1-1 install ok installed r-cran-promises r-cran-promises 1.3.2+dfsg-1 install ok installed r-cran-proxy r-cran-proxy 0.4-27-1 install ok installed r-cran-purrr r-cran-purrr 1.0.4-1 install ok installed r-cran-quantreg r-cran-quantreg 6.1-1 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 1.27.0-1 install ok installed r-cran-r.utils r-cran-r.utils 2.13.0-1 install ok installed r-cran-r6 r-cran-r6 2.6.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rbibutils r-cran-rbibutils 2.3-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.14-1 install ok installed r-cran-rcpparmadillo r-cran-rcpparmadillo 14.4.1-1-1 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-rdpack r-cran-rdpack 2.6.3-1 install ok installed r-cran-readr r-cran-readr 2.1.5-1 install ok installed r-cran-readxl r-cran-readxl 1.4.5-1 install ok installed r-cran-recipes r-cran-recipes 1.1.0+dfsg-1 install ok installed r-cran-reformulas r-cran-reformulas 0.4.0-2 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 1.1.5-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.29+dfsg-1 install ok installed r-cran-rpart r-cran-rpart 4.1.24-1 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 1.10.0+dfsg-2 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-sparsevctrs r-cran-sparsevctrs 0.2.0-2 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+b1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-survival r-cran-survival 3.8-3-1 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-3 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 0.56-1 install ok installed r-cran-tzdb r-cran-tzdb 0.5.0-1 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 1.5.3-1 install ok installed r-cran-xfun r-cran-xfun 0.51+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.18-1 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 2.3.2-1 install ok installed readline-common readline-common 8.2-6 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed salmon salmon 1.10.2+ds1-1+b5 install ok installed samtools samtools 1.21-1 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+b2 install ok installed snakemake snakemake 7.32.4-7 install ok installed sphinx-common sphinx-common 8.1.3-5 install ok installed sqv sqv 1.3.0-1 install ok installed systemd systemd 257.5-2 install ok installed systemd-sysv systemd-sysv 257.5-2 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-8 install ok installed trim-galore trim-galore 0.6.10-1 install ok installed tzdata tzdata 2025b-1 install ok installed ucf ucf 3.0051 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed unzip unzip 6.0-29 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-3 install ok installed x11-common x11-common 1:7.7+24 install ok installed xdg-utils xdg-utils 1.2.1-2 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 1m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'remove', '--allow-remove-essential', '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', 'junit4', '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', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-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', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libezmorph-java', 'libffi8:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgcrypt20: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', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjaxen-java', '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-java', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib: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', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtasn1-6: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', 'libunistring5: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-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', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'libzopfli1', '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', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', '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-numpy-dev:amd64', '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-pytz', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', '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-zopfli', 'python3.13', 'python3.13-minimal', '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-rbibutils', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-rdpack', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-reformulas', '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-sparsevctrs', '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', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 2m3.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: 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 junit4 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 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-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 libdrm2 libedit2 libelf1t64 libepoxy0 liberror-perl libexpat1 libezmorph-java libffi8 libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgcrypt20 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgnutls30t64 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libhamcrest-java libharfbuzz0b libhts3t64 libhtscodecs2 libhtsjdk-java libhwasan0 libhwloc15 libice6 libicu76 libidn2-0 libimagequant0 libisal2 libitm1 libjaxen-java 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-java libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap2 liblerc4 libllvm19 liblsan0 liblua5.4-0 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-ngs3 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libnspr4 libnss3 libnuma1 libopenjp2-7 libp11-kit0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpciaccess0 libpcsclite1 libperl5.40 libpixman-1-0 libpng16-16t64 libpsl5t64 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libstaden-read14t64 libstdc++-14-dev libsystemd-shared libtasn1-6 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxom-java libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 libzopfli1 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 python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-attr python3-autocommand python3-babel python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-click 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-numpy-dev 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-pytz python3-ratelimiter python3-referencing python3-requests python3-retry python3-rich python3-rich-click python3-roman python3-rpds-py python3-scipy 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-zopfli python3.13 python3.13-minimal 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-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 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-sparsevctrs 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 sgml-base shared-mime-info snakemake sphinx-common systemd systemd-sysv tk8.6-blt2.5 trim-galore unicode-data unzip x11-common xdg-utils xkb-data xml-core zip zlib1g-dev WARNING: The following essential packages will be removed. This should NOT be done unless you know exactly what you are doing! systemd-sysv systemd (due to systemd-sysv) 0 upgraded, 0 newly installed, 665 to remove and 0 not upgraded. After this operation, 2290 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 ... 99115 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 (21.0.7~8ea-1) ... Removing libgtk-3-0t64:amd64 (3.24.49-3) ... Removing adwaita-icon-theme (48.0-1) ... Removing libatk-bridge2.0-0t64:amd64 (2.56.1-2) ... Removing libatk1.0-0t64:amd64 (2.56.1-2) ... Removing at-spi2-common (2.56.1-2) ... Removing multiqc (1.21+dfsg-2) ... Removing python3-deeptools (3.5.6+dfsg-1) ... Removing python3-matplotlib (3.10.1+dfsg1-2) ... Removing python3-pil.imagetk:amd64 (11.1.0-5+b1) ... Removing python3-pil:amd64 (11.1.0-5+b1) ... Removing python3-tk:amd64 (3.13.3-1) ... Removing blt (2.5.3+dfsg-8) ... Removing snakemake (7.32.4-7) ... Removing python3-numpydoc (1.8.0-1) ... Removing python3-sphinx (8.1.3-5) ... Removing libhtsjdk-java (4.1.3+dfsg-2) ... Removing libjson-java (3.1.0+dfsg-2) ... Removing junit4 (4.13.2-5) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.7~8ea-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-2) ... Removing coinor-libcoinutils3v5:amd64 (2.11.11+ds-5) ... Removing trim-galore (0.6.10-1) ... Removing cutadapt (4.7-2) ... Removing libgtk-3-common (3.24.49-3) ... Removing dconf-gsettings-backend:amd64 (0.40.0-5) ... Removing dconf-service (0.40.0-5) ... Removing dbus-user-session (1.16.2-2) ... Removing libpam-systemd:amd64 (257.5-2) ... Removing dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-daemon (1.16.2-2) ... Removing dbus-bin (1.16.2-2) ... Removing dbus-session-bus-common (1.16.2-2) ... Removing dbus-system-bus-common (1.16.2-2) ... Removing python3-docutils (0.21.2+dfsg-2) ... Removing docutils-common (0.21.2+dfsg-2) ... Removing fastp (0.24.0+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 (6.1-1) ... Removing r-cran-conquer (1.3.3-1) ... Removing r-cran-caret (7.0-1+dfsg-1) ... Removing r-cran-recipes (1.1.0+dfsg-1) ... Removing r-cran-ipred (0.9-15-1) ... Removing r-cran-rpart (4.1.24-1) ... Removing r-cran-prodlim (2024.06.25-1) ... Removing r-cran-pbkrtest (0.5.3-1) ... Removing r-cran-lme4 (1.1-37-1) ... Removing r-cran-reformulas (0.4.0-2) ... Removing r-bioc-rtracklayer (1.66.0-2) ... Removing r-bioc-genomicalignments (1.42.0-2) ... Removing r-bioc-deseq2 (1.46.0+dfsg-2) ... Removing r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... Removing r-bioc-delayedarray (0.32.0+dfsg-2) ... Removing r-bioc-sparsearray (1.6.2+dfsg-2) ... Removing r-bioc-s4arrays (1.6.0+dfsg-2) ... Removing r-cran-abind (1.4-8-1) ... Removing r-bioc-rsamtools (2.22.0+dfsg-2) ... Removing r-bioc-biocparallel (1.40.0-2) ... 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-8) ... Removing python3.13-tk (3.13.3-1) ... Removing libcairo-gobject2:amd64 (1.18.4-1+b1) ... Removing python-matplotlib-data (3.10.1+dfsg1-2) ... 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 (2.29+dfsg-1) ... Removing r-cran-knitr (1.50+dfsg-1) ... Removing r-cran-crosstalk (1.2.1+dfsg-1) ... Removing fonts-lyx (2.4.3-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing python3-git (3.1.44-1) ... Removing git (1:2.49.0-1) ... Removing git-man (1:2.49.0-1) ... Removing gtk-update-icon-cache (4.18.4+ds-1) ... Removing hicolor-icon-theme (0.18-2) ... Removing hisat2 (2.2.1-5+b3) ... Removing java-common (0.76) ... Removing libcommons-beanutils-java (1.9.4-2) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libcommons-logging-java (1.3.0-1) ... Removing libcommons-lang3-java (3.17.0-1) ... dpkg: warning: overriding problem because --force enabled: dpkg: warning: this is a protected package; it should not be removed Removing systemd-sysv (257.5-2) ... Removing systemd (257.5-2) ... Removing libapparmor1:amd64 (4.1.0~beta5-6) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-4.2) ... Removing libstdc++-14-dev:amd64 (14.2.0-19) ... Removing libgcc-14-dev:amd64 (14.2.0-19) ... Removing libasan8:amd64 (14.2.0-19) ... Removing libasound2t64:amd64 (1.2.13-1+b1) ... Removing libasound2-data (1.2.13-1) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... Removing shared-mime-info (2.4-5+b2) ... Removing libcloudproviders0:amd64 (0.3.6-2) ... Removing libatspi2.0-0t64:amd64 (2.56.1-2) ... Removing libcups2t64:amd64 (2.4.10-2+b1) ... Removing libavahi-client3:amd64 (0.8-16) ... Removing libavahi-common3:amd64 (0.8-16) ... Removing libavahi-common-data:amd64 (0.8-16) ... Removing python3-pybigwig (0.3.23+dfsg-1+b3) ... Removing megadepth (1.2.0-4+b1) ... Removing libbigwig0t64:amd64 (0.4.7+dfsg-3.1+b2) ... Removing r-cran-rcpparmadillo (14.4.1-1-1) ... Removing python3-spectra (0.1.0-1) ... Removing python3-colormath (3.0.0-4) ... Removing python3-htseq (2.0.9+dfsg-1+b2) ... Removing r-cran-ggsignif (0.6.4-1) ... Removing salmon (1.10.2+ds1-1+b5) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Removing libboost-iostreams1.83.0:amd64 (1.83.0-4.2) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Removing libraqm0:amd64 (0.10.2-1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-rcurl (1.98-1.16+dfsg-1) ... Removing r-bioc-biostrings (2.74.1+dfsg-2) ... Removing r-bioc-genomicranges (1.58.0+dfsg-2) ... Removing r-bioc-xvector (0.46.0-2) ... Removing r-bioc-rhtslib (3.2.0+dfsg-2) ... Removing r-bioc-zlibbioc (1.52.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libc6-dev:amd64 (2.41-6) ... Removing libc-dev-bin (2.41-6) ... Removing libcolord2:amd64 (1.4.7-3) ... Removing libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Removing libcommons-compress-java (1.27.1-2) ... Removing libcommons-codec-java (1.18.0-1) ... Removing libcommons-collections3-java (3.2.2-3) ... Removing libcommons-collections4-java (4.4-2) ... Removing libcommons-io-java (2.18.0-1) ... Removing libcommons-math3-java (3.6.1-4) ... Removing libcrypt-dev:amd64 (1:4.4.38-1) ... Removing python3-datrie:amd64 (0.8.2-5+b2) ... Removing libdbus-1-3:amd64 (1.16.2-2) ... Removing libdconf1:amd64 (0.40.0-5) ... Removing samtools (1.21-1) ... Removing libgl1:amd64 (1.7.0-1+b2) ... Removing libglx0:amd64 (1.7.0-1+b2) ... Removing libglx-mesa0:amd64 (25.0.3-1) ... Removing libgl1-mesa-dri:amd64 (25.0.3-1) ... Removing libgbm1:amd64 (25.0.3-1) ... Removing mesa-libgallium:amd64 (25.0.3-1) ... Removing libdrm-amdgpu1:amd64 (2.4.124-2) ... Removing libdrm-intel1:amd64 (2.4.124-2) ... Removing libdrm2:amd64 (2.4.124-2) ... Removing libdrm-common (2.4.124-2) ... Removing libllvm19:amd64 (1:19.1.7-3) ... Removing libedit2:amd64 (3.1-20250104-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libepoxy0:amd64 (1.5.10-2) ... Removing liberror-perl (0.17030-1) ... Removing python3-plotly (5.20.0+dfsg-1) ... Removing python3-nbformat (5.9.1-1) ... Removing python3-jsonschema (4.19.2-6) ... Removing python3-jsonschema-specifications (2023.12.1-2) ... Removing python3-referencing (0.36.2-1) ... Removing python3-rpds-py (0.21.0-2+b1) ... Removing python3-yte (1.5.4-1) ... Removing python3-rich-click (1.6.0-2) ... Removing python3-rich (13.9.4-1) ... Removing python3-coloredlogs (15.0.1-1) ... Removing python3-humanfriendly (10.0-6) ... 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Removing r-cran-rio (1.2.3-1) ... Removing libhamcrest-java (2.2-2) ... Removing libhwasan0:amd64 (14.2.0-19) ... Removing libtbb12:amd64 (2022.1.0-1) ... Removing libtbbbind-2-5:amd64 (2022.1.0-1) ... Removing libhwloc15:amd64 (2.12.0-1) ... Removing r-cran-doby (4.6.25-1) ... 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 (4.2.8-1) ... Removing r-cran-stringi (1.8.4-1+b1) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libisal2 (2.31.1-1.1) ... Removing libitm1:amd64 (14.2.0-19) ... Removing libxom-java (1.3.9-1) ... Removing libjaxen-java (1.1.6-5) ... Removing libjbzip2-java (0.9.1-8) ... Removing libjemalloc2:amd64 (5.3.0-3) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-sphinxdoc (8.1.3-5) ... Removing libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... 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Removing libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Removing libxcb-sync1:amd64 (1.17.0-2+b1) ... Removing libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Removing libxcb-glx0:amd64 (1.17.0-2+b1) ... Removing libxcb-present0:amd64 (1.17.0-2+b1) ... Removing libxcb-randr0:amd64 (1.17.0-2+b1) ... Removing libxcomposite1:amd64 (1:0.4.6-1) ... Removing libxcursor1:amd64 (1:1.2.3-1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b2) ... Removing libxerces2-java (2.12.2-1) ... Removing libxfixes3:amd64 (1:6.0.0-2+b4) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b4) ... Removing libxkbcommon0:amd64 (1.7.0-2) ... Removing libxml-commons-external-java (1.4.01-6) ... Removing libxml-commons-resolver1.1-java (1.2-11) ... Removing r-cran-xml (3.99-0.18-1) ... Removing libxrandr2:amd64 (2:1.5.4-1+b3) ... Removing libxshmfence1:amd64 (1.3.3-1) ... Removing libyaml-0-2:amd64 (0.2.5-2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing linux-libc-dev (6.12.21-1) ... 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Removing r-cran-timechange (0.3.0-1) ... Removing r-cran-cpp11 (0.5.2-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-curl (6.2.1+dfsg-1) ... Removing r-cran-modelmetrics (1.2.2.2-1+b1) ... Removing r-cran-deriv (4.1.6-1) ... Removing r-cran-diagram (1.6.5-2) ... Removing r-cran-progressr (0.15.1-1) ... Removing r-cran-forcats (1.0.0-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (1.0.3-1) ... Removing r-cran-foreign (0.8.90-1) ... 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 (0.9.6-1) ... Removing r-cran-purrr (1.0.4-1) ... 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 (2.23-26-1) ... Removing r-cran-locfit (1.5-9.12-1) ... Removing r-cran-lazyeval (0.2.2-1+b1) ... Removing r-cran-listenv (0.9.1+dfsg-1) ... Removing r-cran-matrixmodels (0.5-4-1) ... Removing r-cran-matrixstats (1.5.0-1) ... Removing r-cran-microbenchmark (1.5.0-1) ... Removing r-cran-minqa (1.2.8-1) ... Removing r-cran-nnet (7.3-20-1) ... Removing r-cran-numderiv (2016.8-1.1-3) ... Removing r-cran-parallelly (1.42.0-1) ... 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 (2.13.0-1) ... Removing r-cran-r.oo (1.27.0-1) ... Removing r-cran-r.methodss3 (1.8.2-1) ... Removing r-cran-rdpack (2.6.3-1) ... Removing r-cran-rbibutils (2.3-1) ... 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 (0.56-1) ... Removing r-cran-writexl (1.5.3-1) ... Removing r-cran-xfun (0.51+dfsg-1) ... Removing r-cran-yaml (2.3.10-1) ... Removing r-cran-zip (2.3.2-1) ... 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-5) ... Removing r-cran-survival (3.8-3-1) ... Removing r-cran-shiny (1.10.0+dfsg-2) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-bslib (0.9.0+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (12) ... 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 (1.9-3-1) ... Removing libhts3t64:amd64 (1.21+ds-1) ... Removing python3-pkg-resources (75.8.0-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.2-1) ... Removing r-cran-data.table (1.17.0+dfsg-1) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... 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 r-cran-httpuv (1.6.15+dfsg-1) ... Removing r-cran-sass (0.4.9+dfsg-1) ... Removing r-cran-fs (1.6.5+dfsg-1) ... Removing libuv1t64:amd64 (1.50.0-2) ... 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-autocommand (2.2.2-3) ... Removing python3-certifi (2025.1.31+ds-1) ... Removing python3-chardet (5.2.0+dfsg-2) ... Removing python3-charset-normalizer (3.4.1-1+b1) ... Removing python3-idna (3.10-1) ... Removing python3-jaraco.context (6.0.1-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.6.0-1) ... Removing python3-typing-extensions (4.13.1-1) ... Removing python3-urllib3 (2.3.0-2) ... Removing r-bioc-s4vectors (0.44.0+dfsg-2) ... Removing r-bioc-biocgenerics (0.52.0-2) ... Removing r-cran-fontawesome (0.5.3-1) ... 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-3) ... 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 (1.9.5-1) ... Removing r-cran-crayon (1.5.3-1) ... Removing r-cran-digest (0.6.37-1) ... Removing r-cran-fansi (1.0.6-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-promises (1.3.2+dfsg-1) ... Removing r-cran-fastmap (1.2.0-1) ... Removing r-cran-pillar (1.10.1+dfsg-1) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.9.1+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-later (1.4.1+dfsg-1) ... Removing r-cran-nlme (3.1.168-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-65-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-r6 (2.6.1-1) ... 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 (1.7-3-1) ... Removing r-cran-rcpp (1.0.14-1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing libcurl3t64-gnutls:amd64 (8.13.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.8.0-1) ... Removing r-cran-lattice (0.22-7-1) ... Removing r-cran-littler (0.3.21-1) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-rlang (1.1.5-1) ... Removing r-cran-cli (3.6.4-1) ... Removing r-base-core (4.4.3-1+b1) ... Removing libpangocairo-1.0-0:amd64 (1.56.3-1) ... Removing libpangoft2-1.0-0:amd64 (1.56.3-1) ... Removing libpango-1.0-0:amd64 (1.56.3-1) ... Removing fontconfig (2.15.0-2.3) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b4) ... Removing libcairo2:amd64 (1.18.4-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-2.3) ... Removing fontconfig-config (2.15.0-2.3) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.13.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libtirpc3t64:amd64 (1.3.6+ds-1) ... 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 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-1+b1) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.7.0-3) ... Removing libdeflate0:amd64 (1.23-1+b1) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libgnutls30t64:amd64 (3.8.9-2) ... Removing libgomp1:amd64 (14.2.0-19) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Removing libsm6:amd64 (2:1.2.6-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libicu76:amd64 (76.1-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-5) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing libldap2:amd64 (2.6.9+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libpaper-utils (2.2.5-0.3+b2) ... Removing libpaper2:amd64 (2.2.5-0.3+b2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.47-1.1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.6+ds-1) ... Removing libunistring5:amd64 (1.3-2) ... 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+b3) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing libxrender1:amd64 (1:0.9.12-1) ... Removing unzip (6.0-29) ... Removing x11-common (1:7.7+24) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.2.1-2) ... Removing zip (3.0-14) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libglib2.0-0t64:amd64 (2.84.1-1) ... Removing libatomic1:amd64 (14.2.0-19) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing openssl (3.5.0-1) ... Removing python3-ufolib2 (0.17.1+dfsg1-1) ... Removing python3-attr (25.3.0-1) ... Removing python3-fonttools (4.57.0-1) ... Removing python3-scipy (1.15.2-7) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing python3-lxml:amd64 (5.3.2-1) ... Removing libxslt1.1:amd64 (1.1.35-1.2) ... Removing libgcrypt20:amd64 (1.11.0-7) ... Removing liblapack3:amd64 (3.12.1-2) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libgpg-error0:amd64 (1.51-4) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Removing python3-zopfli (0.2.3.post1-1+b1) ... Removing libzopfli1 (1.0.3-3) ... Removing python3-brotli (1.1.0-2+b7) ... Removing python3-decorator (5.2.1-1) ... Removing python3-fs (2.4.16-7) ... Removing python3-lz4 (4.4.0+dfsg-2) ... Removing python3-sympy (1.13.3-5) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing python3-platformdirs (4.3.7-1) ... Removing python3-unicodedata2 (15.1.0+ds-1+b4) ... Removing unicode-data (15.1.0-1) ... Removing libblas3:amd64 (3.12.1-2) ... Removing python3 (3.13.3-1) ... Removing python3-minimal (3.13.3-1) ... Removing python3.13 (3.13.3-1) ... Removing python3.13-minimal (3.13.3-1) ... Removing libexpat1:amd64 (2.7.1-1) ... Removing libpython3-stdlib:amd64 (3.13.3-1) ... Removing libpython3.13-stdlib:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libpython3.13-minimal:amd64 (3.13.3-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... 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 media-types (13.0.0) ... Removing netbase (6.5) ... Removing readline-common (8.2-6) ... Removing libffi8:amd64 (3.4.7-1) ... Processing triggers for procps (2:4.0.4-7) ... Processing triggers for libc-bin (2.41-6) ... 2m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'remove', '--allow-remove-essential', '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', 'junit4', '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', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-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', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libezmorph-java', 'libffi8:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgcrypt20: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', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjaxen-java', '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-java', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib: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', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtasn1-6: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', 'libunistring5: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-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', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'libzopfli1', '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', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', '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-numpy-dev:amd64', '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-pytz', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', '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-zopfli', 'python3.13', 'python3.13-minimal', '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-rbibutils', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-rdpack', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-reformulas', '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-sparsevctrs', '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', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 2m3.4s INFO: Running scripts post_remove 2m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_remove_cleanup'] 2m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_remove_cleanup'] 2m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_remove_exceptions'] 2m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_remove_exceptions'] 2m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', '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', 'junit4', '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', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-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', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libezmorph-java', 'libffi8:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgcrypt20: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', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjaxen-java', '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-java', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib: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', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtasn1-6: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', 'libunistring5: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-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', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'libzopfli1', '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', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', '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-numpy-dev:amd64', '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-pytz', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', '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-zopfli', 'python3.13', 'python3.13-minimal', '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-rbibutils', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-rdpack', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-reformulas', '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-sparsevctrs', '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', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 2m3.8s DUMP: (Reading database ... 5615 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (48.0-1) ... 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 (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. 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isn't installed dpkg: warning: ignoring request to remove libgbm1 which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed dpkg: warning: ignoring request to remove libgcrypt20 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-2) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (25.0.3-1) ... 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installed Purging configuration files for libpaper2:amd64 (2.2.5-0.3+b2) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.13 which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.3-1) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which 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configuration files for libxml-commons-resolver1.1-java (1.2-11) ... dpkg: warning: while removing libxml-commons-resolver1.1-java, directory '/etc/xml' not empty so not removed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxom-java which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove libzopfli1 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed Purging configuration files for media-types (13.0.0) ... dpkg: warning: ignoring request to remove megadepth which isn't installed dpkg: warning: ignoring request to remove mesa-libgallium which isn't installed dpkg: warning: ignoring request to remove multiqc which isn't installed dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed Purging configuration files for netbase (6.5) ... dpkg: warning: ignoring request to remove node-bootstrap-sass which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove node-normalize.css which isn't installed dpkg: warning: ignoring request to remove openjdk-21-jre which isn't installed Purging configuration files for openjdk-21-jre-headless:amd64 (21.0.7~8ea-1) ... Purging configuration files for openssl (3.5.0-1) ... dpkg: warning: ignoring request to remove pandoc which isn't installed dpkg: warning: ignoring request to remove pandoc-data which isn't installed Purging configuration files for perl (5.40.1-2) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed dpkg: warning: ignoring request to remove pigz which isn't installed dpkg: warning: ignoring request to remove python-babel-localedata which isn't installed Purging configuration files for python-matplotlib-data (3.10.1+dfsg1-2) ... Purging configuration files for python3 (3.13.3-1) ... dpkg: warning: ignoring request to remove python3-alabaster which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-babel which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-click which isn't installed dpkg: warning: ignoring request to remove python3-coloredlogs which isn't installed dpkg: warning: ignoring request to remove python3-colormath which isn't installed dpkg: warning: ignoring request to remove 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python3-docutils which isn't installed dpkg: warning: ignoring request to remove python3-dpath which isn't installed dpkg: warning: ignoring request to remove python3-fastjsonschema which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-git which isn't installed dpkg: warning: ignoring request to remove python3-gitdb which isn't installed dpkg: warning: ignoring request to remove python3-htseq which isn't installed dpkg: warning: ignoring request to remove python3-humanfriendly which isn't installed dpkg: warning: ignoring request to remove python3-humanize which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-imagesize which isn't installed dpkg: warning: ignoring request to remove python3-importlib-metadata which isn't 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remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-smart-open which isn't installed dpkg: warning: ignoring request to remove python3-smmap which isn't installed dpkg: warning: ignoring request to remove python3-snowballstemmer which isn't installed dpkg: warning: ignoring request to remove python3-spectra which isn't installed dpkg: warning: ignoring request to remove python3-sphinx which isn't installed dpkg: warning: ignoring request to remove python3-stopit which isn't installed Purging configuration files for python3-sympy (1.13.3-5) ... dpkg: warning: ignoring request to remove python3-tabulate which isn't installed dpkg: warning: ignoring request to remove python3-tenacity which isn't installed dpkg: warning: ignoring request to remove python3-throttler which isn't installed dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-toposort which isn't installed dpkg: 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python3-zopfli which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.3-1) ... dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for r-base-core (4.4.3-1+b1) ... dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-deseq2 which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicalignments which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-tximport which isn't installed dpkg: warning: ignoring request to remove r-bioc-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-backports which isn't installed dpkg: warning: ignoring request to remove r-cran-base64enc which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-boot which isn't installed dpkg: warning: ignoring request to remove r-cran-broom which isn't installed dpkg: warning: ignoring request to remove r-cran-bslib which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-car which isn't installed dpkg: warning: ignoring request to remove r-cran-cardata which isn't installed dpkg: warning: ignoring request to remove r-cran-caret which isn't installed dpkg: warning: ignoring request to remove r-cran-cellranger which isn't installed dpkg: warning: ignoring request to remove r-cran-class which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-clipr which isn't installed dpkg: warning: ignoring request to remove r-cran-clock which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-colourpicker which isn't installed dpkg: warning: ignoring request to remove r-cran-commonmark which isn't installed dpkg: warning: ignoring request to remove r-cran-conquer which isn't installed dpkg: warning: ignoring request to remove r-cran-corrplot which isn't installed dpkg: warning: ignoring request to remove r-cran-cowplot which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-crosstalk which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-data.table which isn't installed dpkg: warning: ignoring request to remove r-cran-deriv which isn't installed dpkg: warning: ignoring request to remove r-cran-diagram which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-doby which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-dt which isn't installed dpkg: warning: ignoring request to remove r-cran-e1071 which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-fontawesome which isn't installed dpkg: warning: ignoring request to remove r-cran-forcats which isn't installed dpkg: warning: ignoring request to remove r-cran-foreach which isn't installed dpkg: warning: ignoring request to remove r-cran-foreign which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-formula which isn't installed dpkg: warning: ignoring request to remove r-cran-fs which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-future which isn't installed dpkg: warning: ignoring request to remove r-cran-future.apply which isn't installed dpkg: warning: ignoring request to remove r-cran-generics which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-ggpubr which isn't installed dpkg: warning: ignoring request to remove r-cran-ggrepel which isn't installed dpkg: warning: ignoring request to remove r-cran-ggsci which isn't installed dpkg: warning: ignoring request to remove r-cran-ggsignif which isn't installed dpkg: warning: ignoring request to remove r-cran-globals which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-gower which isn't installed dpkg: warning: ignoring request to remove r-cran-gprofiler2 which isn't installed dpkg: warning: ignoring request to remove r-cran-gridextra which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-hardhat which isn't installed dpkg: warning: ignoring request to remove r-cran-haven which isn't installed dpkg: warning: ignoring request to remove r-cran-highr which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-htmltools which isn't installed dpkg: warning: ignoring request to remove r-cran-htmlwidgets which isn't installed dpkg: warning: ignoring request to remove r-cran-httpuv which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-ipred which isn't installed dpkg: warning: ignoring request to remove r-cran-isoband which isn't installed dpkg: warning: ignoring request to remove r-cran-iterators which isn't installed dpkg: warning: ignoring request to remove r-cran-jquerylib which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-kernsmooth which isn't installed dpkg: warning: ignoring request to remove r-cran-knitr which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-later which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lava which isn't installed dpkg: warning: ignoring request to remove r-cran-lazyeval which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-listenv which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-lme4 which isn't installed dpkg: warning: ignoring request to remove r-cran-locfit which isn't installed dpkg: warning: ignoring request to remove r-cran-lubridate which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixmodels which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-microbenchmark which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-miniui which isn't installed dpkg: warning: ignoring request to remove r-cran-minqa which isn't installed dpkg: warning: ignoring request to remove r-cran-modelmetrics which isn't installed dpkg: warning: ignoring request to remove r-cran-modelr which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-nloptr which isn't installed dpkg: warning: ignoring request to remove r-cran-nnet which isn't installed dpkg: warning: ignoring request to remove r-cran-numderiv which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-openxlsx which isn't installed dpkg: warning: ignoring request to remove r-cran-parallelly which isn't installed dpkg: warning: ignoring request to remove r-cran-pbkrtest which isn't installed dpkg: warning: ignoring request to remove r-cran-pheatmap which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plotly which isn't installed dpkg: warning: ignoring request to remove r-cran-plyr which isn't installed dpkg: warning: ignoring request to remove r-cran-polynom which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-proc which isn't installed dpkg: warning: ignoring request to remove r-cran-prodlim which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-progressr which isn't installed dpkg: warning: ignoring request to remove r-cran-promises which isn't installed dpkg: warning: ignoring request to remove r-cran-proxy which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-quantreg which isn't installed dpkg: warning: ignoring request to remove r-cran-r.methodss3 which isn't installed dpkg: warning: ignoring request to remove r-cran-r.oo which isn't installed dpkg: warning: ignoring request to remove r-cran-r.utils which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rbibutils which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpparmadillo which isn't installed dpkg: warning: ignoring request to remove r-cran-rcppeigen which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-rdpack which isn't installed dpkg: warning: ignoring request to remove r-cran-readr which isn't installed dpkg: warning: ignoring request to remove r-cran-readxl which isn't installed dpkg: warning: ignoring request to remove r-cran-recipes which isn't installed dpkg: warning: ignoring request to remove r-cran-reformulas which isn't installed dpkg: warning: ignoring request to remove r-cran-rematch which isn't installed dpkg: warning: ignoring request to remove r-cran-reshape2 which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rio which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rmarkdown which isn't installed dpkg: warning: ignoring request to remove r-cran-rpart which isn't installed dpkg: warning: ignoring request to remove r-cran-rstatix which isn't installed dpkg: warning: ignoring request to remove r-cran-sass which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-shape which isn't installed dpkg: warning: ignoring request to remove r-cran-shiny which isn't installed dpkg: warning: ignoring request to remove r-cran-shinyjs which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-sourcetools which isn't installed dpkg: warning: ignoring request to remove r-cran-sparsem which isn't installed dpkg: warning: ignoring request to remove r-cran-sparsevctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-squarem which isn't installed dpkg: warning: ignoring request to remove r-cran-statmod which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-survival which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-timechange which isn't installed dpkg: warning: ignoring request to remove r-cran-timedate which isn't installed dpkg: warning: ignoring request to remove r-cran-tinytex which isn't installed dpkg: warning: ignoring request to remove r-cran-tzdb which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-vroom which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-writexl which isn't installed dpkg: warning: ignoring request to remove r-cran-xfun which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xtable which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed dpkg: warning: ignoring request to remove r-cran-zip which isn't installed Purging configuration files for readline-common (8.2-6) ... 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 Purging configuration files for sgml-base (1.31) ... Purging configuration files for shared-mime-info (2.4-5+b2) ... 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 (257.5-2) ... 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 dpkg: warning: ignoring request to remove unicode-data which isn't installed dpkg: warning: ignoring request to remove unzip which isn't installed Purging configuration files for x11-common (1:7.7+24) ... 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 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', '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', 'junit4', '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', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-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', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'liberror-perl', 'libexpat1:amd64', 'libezmorph-java', 'libffi8:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgcrypt20: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', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgpg-error0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libhamcrest-java', 'libharfbuzz0b:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libimagequant0:amd64', 'libisal2', 'libitm1:amd64', 'libjaxen-java', '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-java', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnlopt0:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenjp2-7:amd64', 'libp11-kit0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib: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', 'libslf4j-java', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libtasn1-6: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', 'libunistring5: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-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', 'libxerces2-java', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2:amd64', 'libxom-java', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'libzopfli1', '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', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-alabaster', 'python3-attr', 'python3-autocommand', 'python3-babel', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', '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-numpy-dev:amd64', '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-pytz', 'python3-ratelimiter', 'python3-referencing', 'python3-requests', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-rpds-py', 'python3-scipy', '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-zopfli', 'python3.13', 'python3.13-minimal', '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-rbibutils', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-rdpack', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-reformulas', '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-sparsevctrs', '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', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'trim-galore', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', 'pigx-rnaseq'] 2m3.8s DUMP: dpkg: warning: ignoring request to remove pigx-rnaseq which isn't installed 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', 'pigx-rnaseq'] 2m3.8s INFO: Running scripts post_purge 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_purge_exceptions'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_purge_exceptions'] 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_purge_manual_cleanup'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_purge_manual_cleanup'] 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', '--pending'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--purge', '--pending'] 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--remove', '--pending'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg', '--remove', '--pending'] 2m3.8s INFO: Running scripts post_test 2m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_test_exceptions'] 2m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'tmp/scripts/post_test_exceptions'] 2m3.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 2m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 2m4.0s INFO: IGNORED broken symlink: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 2m4.0s INFO: IGNORED broken symlink: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 2m4.2s DEBUG: No broken symlinks as far as we can find. 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-divert', '--list'] 2m4.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 /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 2m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'dpkg-divert', '--list'] 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 2m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmps0rc_fks', 'apt-get', 'clean'] 2m4.3s DEBUG: Recording chroot state 2m4.5s INFO: IGNORED PATH@1: /var/lib/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.5s INFO: IGNORED PATH@1: /var/lib/systemd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.5s INFO: IGNORED PATH@1: /var/cache/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.5s INFO: IGNORED PATH@1: /var/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.5s INFO: IGNORED PATH@1: /var/spool/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.6s INFO: IGNORED PATH@1: /root/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 2m4.6s INFO: IGNORED PATH@1: /run/lock/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 2m4.6s INFO: IGNORED PATH@2: /var/lib/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.6s INFO: IGNORED PATH@2: /var/lib/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /var/lib/systemd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /var/cache/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.6s INFO: IGNORED PATH@2: /var/cache/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /var/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.6s INFO: IGNORED PATH@2: /var/log/private/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /var/spool/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/var.conf) 2m4.6s INFO: IGNORED PATH@2: /etc/vconsole.conf (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 2m4.6s INFO: IGNORED PATH@2: /etc/default/locale (flag L+ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 2m4.6s INFO: IGNORED PATH@2: /root/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 2m4.6s INFO: IGNORED PATH@2: /root/.ssh/ (flag d- systemd-tmpfiles snippet /usr/lib/tmpfiles.d/provision.conf) 2m4.6s INFO: IGNORED PATH@2: /run/log/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/user/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/shutdown/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/machines/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/users/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/sessions/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/seats/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/ask-password/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/netif/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/netif/leases/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 2m4.6s INFO: IGNORED PATH@2: /run/systemd/netif/links/ (flag d$ systemd-tmpfiles snippet /usr/lib/tmpfiles.d/systemd-network.conf) 2m4.6s INFO: IGNORED PATH@2: /run/sendsigs.omit.d/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/debian.conf) 2m4.6s INFO: IGNORED PATH@2: /run/sshd/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/20-systemd-ssh-generator.conf) 2m4.6s INFO: IGNORED PATH@2: /run/lock/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 2m4.6s INFO: IGNORED PATH@2: /run/lock/subsys/ (flag d systemd-tmpfiles snippet /usr/lib/tmpfiles.d/legacy.conf) 2m6.4s INFO: PASS: Installation and purging test. 2m6.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/shm'] 2m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/shm'] 2m6.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/console'] 2m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/console'] 2m6.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/ptmx'] 2m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/ptmx'] 2m6.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/pts'] 2m6.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/dev/pts'] 2m6.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/proc'] 2m6.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmps0rc_fks/proc'] 2m6.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 2m6.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmps0rc_fks'] 2m6.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmps0rc_fks 2m6.8s INFO: PASS: All tests. 2m6.8s INFO: piuparts run ends. ret=0 End: 2025-04-09 18:14:11 GMT