Start: 2024-08-22 10:30:22 GMT [bookworm] Package: pigx-rnaseq Version: 0.1.0-1.1 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 (>= 0.15+dfsg-2), 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_0.1.0-1.1_all.deb Size: 61244 MD5sum: c498fc408d04299178397f05965119df SHA256: 32b5f61115e9fbe559bf2f2dc316127579029f6a4309457906c100956c9ee553 [bookworm-next] Package: pigx-rnaseq Version: 0.1.0-1.1 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 (>= 0.15+dfsg-2), 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_0.1.0-1.1_all.deb Size: 61244 MD5sum: c498fc408d04299178397f05965119df SHA256: 32b5f61115e9fbe559bf2f2dc316127579029f6a4309457906c100956c9ee553 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt pigx-rnaseq=0.1.0-1.1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201135~1.4.3-10-g39df1906 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt pigx-rnaseq=0.1.0-1.1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpcd0u3cip 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpcd0u3cip 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpcd0u3cip/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'update'] 0m1.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s 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' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 0m4.5s INFO: Running scripts is_testable 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s INFO: Running scripts pre_test 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_test_root_password'] 0m4.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_test_root_password'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 0m4.8s DUMP: Package: pigx-rnaseq Version: 0.1.0-1.1 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 (>= 0.15+dfsg-2), 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_0.1.0-1.1_all.deb Size: 61244 MD5sum: c498fc408d04299178397f05965119df SHA256: 32b5f61115e9fbe559bf2f2dc316127579029f6a4309457906c100956c9ee553 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 0m4.8s INFO: apt-cache knows about the following packages: pigx-rnaseq 0m4.8s INFO: Running scripts pre_install 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 0m4.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 0m4.9s DUMP: pigx-rnaseq: Installed: (none) Candidate: 0.1.0-1.1 Version table: 0.1.0-1.1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 4m46.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adwaita-icon-theme at-spi2-common binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cpp cpp-12 cutadapt default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax g++ g++-12 gcc gcc-12 gir1.2-glib-2.0 git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libaec0 libapache-pom-java libargs4j-java libasan8 libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0 libbinutils libblas3 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 liberror-perl libexpat1 libexpat1-dev libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libhtsjdk-java libhwloc15 libice6 libicu72 libimagequant0 libisal2 libisl23 libitm1 libjansson4 libjbig0 libjbzip2-java libjemalloc2 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-metadata libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblsan0 liblua5.3-0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmpc3 libmpfr6 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libnlopt0 libnsl-dev libnsl2 libnspr4 libnss3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsis-base-java libsis-base-jni libsis-jhdf5-java libsis-jhdf5-jni libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsodium23 libsqlite3-0 libssh2-1 libssl3 libstaden-read14 libstdc++-12-dev libsz2 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libuv1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxsimd-dev libxslt1.1 libxss1 libxt6 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev littler media-types megadepth multiqc ncbi-vdb-data node-bootstrap-sass node-html5shiv node-normalize.css openjdk-17-jre openjdk-17-jre-headless openssl pandoc pandoc-data perl perl-modules-5.36 pigz python-babel-localedata python-matplotlib-data python3 python3-adal python3-aiohttp python3-aiosignal python3-alabaster python3-all python3-all-dev python3-appdirs python3-async-timeout python3-attr python3-avro python3-azure python3-azure-storage python3-babel python3-bcrypt python3-beniget python3-blinker python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cryptography python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-dev python3-distutils python3-dnaio python3-docutils python3-fastjsonschema python3-fonttools python3-frozenlist python3-fs python3-future python3-gast python3-gi python3-git python3-gitdb python3-htseq python3-humanfriendly python3-idna python3-imagesize python3-isodate python3-jinja2 python3-jmespath python3-jsonschema python3-jupyter-core python3-jwt python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-marshmallow python3-matplotlib python3-mdurl python3-minimal python3-mpmath python3-msal python3-msal-extensions python3-msrest python3-msrestazure python3-multidict python3-nacl python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-oauthlib python3-packaging python3-paramiko python3-pbr python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-ply python3-portalocker python3-psutil python3-pulp python3-py python3-py2bit python3-pybigwig python3-pygments python3-pyparsing python3-pyrsistent python3-pysam python3-pythran python3-ratelimiter python3-requests python3-requests-oauthlib python3-retry python3-rich python3-rich-click python3-roman python3-ruamel.yaml python3-ruamel.yaml.clib python3-s3transfer python3-scipy python3-setuptools python3-simplejson python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-strictyaml python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-uamqp python3-ufolib2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yarl python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport 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-blob r-cran-boot r-cran-brio r-cran-broom r-cran-bslib r-cran-cachem r-cran-callr 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-dbi r-cran-desc r-cran-diffobj r-cran-digest 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-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-maptools r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics 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-pkgload r-cran-plogr r-cran-plotly r-cran-plyr r-cran-png r-cran-polynom r-cran-praise r-cran-prettyunits r-cran-proc r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstatix r-cran-sass r-cran-scales r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sp r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat 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-waldo r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xml-core zip zlib1g-dev Suggested packages: binutils-doc blt-demo cpp-doc gcc-12-locales cpp-12-doc g++-multilib g++-12-multilib gcc-12-doc gcc-multilib make manpages-dev autoconf automake libtool flex bison gdb gcc-doc gcc-12-multilib gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs git-mediawiki git-svn apache2 | lighttpd | httpd libasound2-plugins alsa-utils libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc libasm-java libxz-java libcommons-io-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java cups-common gdbm-l10n low-memory-monitor krb5-doc krb5-user gvfs picard-tools libhwloc-contrib-plugins libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc liblcms2-utils libngs-java-doc pciutils pcscd rhino lm-sensors libstdc++-12-doc tcl8.6 tk8.6 libxsimd-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 libtap-harness-archive-perl python3-doc python3-venv python-attr-doc python-azure-doc python-blinker-doc python-cryptography-doc python3-cryptography-vectors python-cycler-doc python-python-deeptoolsintervals-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base python-fastjsonschema-doc python-future-doc python-git-doc python-jinja2-doc python-jsonschema-doc python3-pip python3-crypto python-lxml-doc python-markdown-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils python-mpmath-doc python3-gmpy2 python-nacl-doc gfortran python3-pytest python3-gssapi python-pil-doc python3-pandas python3-ipykernel python-ply-doc python-psutil-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-nose python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-plain-generic texlive-fonts-extra python-sympy-doc python-tenacity-doc tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-genefilter r-bioc-go.db r-bioc-org.hs.eg.db r-cran-runit r-bioc-graph r-bioc-biocstyle r-bioc-all r-bioc-affy r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-hdf5array r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-tximeta r-bioc-tximportdata r-cran-pbapply r-bioc-glmgampoi r-cran-biocmanager r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-cran-markdown r-bioc-sparsematrixstats r-bioc-limma r-bioc-rhdf5 r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-aer r-cran-bbmle r-cran-cluster r-cran-cmprsk r-cran-coda 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-rgeos 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-bradleyterry2 r-cran-ellipse r-cran-mlbench r-cran-party r-cran-pls r-cran-randomforest r-cran-rann r-cran-rstudioapi r-cran-whoami r-cran-kernlab r-cran-mvtnorm r-cran-vcd 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-venndiagram r-cran-bench r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-rmysql r-cran-testit r-cran-unitizer r-cran-r.rsp r-cran-profvis r-cran-vdiffr r-cran-tinytest r-cran-th.data r-cran-sf r-cran-rgl r-cran-webshot r-cran-reticulate r-cran-gridsvg r-cran-lintr r-cran-tidyverse r-cran-getopt r-cran-spatstat.geom r-cran-raster r-cran-polyclip r-cran-plotrix r-cran-spatstat.linnet r-cran-spatstat.utils r-cran-spatstat r-cran-r.devices r-cran-formattable r-cran-palmerpenguins r-cran-units r-cran-mathjaxr r-cran-remotes r-cran-ggally r-cran-ggalluvial r-cran-devtools r-cran-dendextend r-cran-irdisplay r-cran-rsvg r-cran-itertools r-cran-pbmcapply r-cran-furrr r-cran-pingr r-cran-inline r-cran-splines2 r-cran-usethis r-cran-downlit r-cran-gert r-cran-gh r-cran-rvest r-cran-dichromat r-cran-rlecuyer r-cran-rgdal r-cran-gstat r-cran-deldir r-cran-pkgbuild r-cran-pkgdown r-cran-zeallot readline-doc cwltool sgml-base-doc slurm-client snakemake-doc debhelper Recommended packages: librsvg2-common patch less ssh-client python3-hisat2 bcftools alsa-ucm-conf alsa-topology-conf curl manpages manpages-dev libc-devtools dbus libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgail-common libgtk2.0-bin libhwloc-plugins node-jquery libjson-xs-perl krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules node-clipboard libjs-filesaver texlive-xetex libatk-wrapper-java-jni fonts-dejavu-extra netbase rna-star python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors python3-bs4 python3-html5lib python3-gdal python3-pydot python3-pygraphviz python3-invoke python3-olefile make isympy-common r-recommended r-base-dev r-doc-html r-cran-thematic r-cran-cliapp r-cran-mockery r-cran-earth r-cran-mda r-cran-mlmetrics r-cran-fastica r-cran-kernlab r-cran-themis r-cran-vdiffr r-cran-decor r-cran-webutils r-cran-covr r-cran-gh r-cran-bench r-cran-dbplyr r-cran-lobstr r-cran-rmysql r-cran-rpostgresql r-cran-rsvg r-cran-testit r-cran-ragg r-cran-hexbin r-cran-hmisc r-cran-interp r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-sf r-cran-svglite r-cran-xml2 r-cran-devtools r-cran-ggbeeswarm r-cran-modeldata r-cran-roxygen2 r-cran-usethis r-cran-markdown r-cran-mlbench r-cran-tikzdevice node-highlight.js r-cran-ellipse r-cran-fields r-cran-geepack r-cran-bookdown r-cran-igraph r-cran-lavasearch2 r-cran-mets r-cran-optimx r-cran-polycor r-cran-rgl r-cran-r.rsp r-cran-zoo r-cran-runit r-cran-sodium r-cran-pkgbuild r-cran-mockr r-cran-ggthemes r-cran-rsclient r-cran-rversions r-cran-domc r-cran-logcondens r-cran-cba r-cran-ddalpha r-cran-dimred r-cran-pls r-cran-rcpproll r-cran-rsample r-cran-rspectra r-cran-rann r-cran-tufte r-cran-dygraphs r-cran-rsconnect r-cran-dbitest r-cran-emmeans r-cran-coin r-cran-spelling r-cran-setrng r-cran-formattable cwltool imagemagick python3-yappi python3-biopython python3-dropbox python3-flask python3-ftputil python3-irodsclient python3-kubernetes 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 binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cpp cpp-12 cutadapt default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax g++ g++-12 gcc gcc-12 gir1.2-glib-2.0 git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libaec0 libapache-pom-java libargs4j-java libasan8 libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0 libbinutils libblas3 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcrypt-dev libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 liberror-perl libexpat1 libexpat1-dev libfindbin-libs-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgdbm-compat4 libgdbm6 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgirepository-1.0-1 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhdf5-103-1 libhts3 libhtscodecs2 libhtsjdk-java libhwloc15 libice6 libicu72 libimagequant0 libisal2 libisl23 libitm1 libjansson4 libjbig0 libjbzip2-java libjemalloc2 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-metadata libjs-jquery-selectize.js libjs-jquery-tablesorter libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-sphinxdoc libjs-twitter-bootstrap-datepicker libjs-underscore libjson-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblsan0 liblua5.3-0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmpc3 libmpfr6 libncbi-ngs3 libncbi-vdb3 libncurses6 libncursesw6 libnghttp2-14 libngs-java libngs-jni libnlopt0 libnsl-dev libnsl2 libnspr4 libnss3 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libquadmath0 libraqm0 libreadline8 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsis-base-java libsis-base-jni libsis-jhdf5-java libsis-jhdf5-jni libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsodium23 libsqlite3-0 libssh2-1 libssl3 libstaden-read14 libstdc++-12-dev libsz2 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libuv1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxshmfence1 libxsimd-dev libxslt1.1 libxss1 libxt6 libxtst6 libxxf86vm1 libyaml-0-2 libz3-4 linux-libc-dev littler media-types megadepth multiqc ncbi-vdb-data node-bootstrap-sass node-html5shiv node-normalize.css openjdk-17-jre openjdk-17-jre-headless openssl pandoc pandoc-data perl perl-modules-5.36 pigx-rnaseq pigz python-babel-localedata python-matplotlib-data python3 python3-adal python3-aiohttp python3-aiosignal python3-alabaster python3-all python3-all-dev python3-appdirs python3-async-timeout python3-attr python3-avro python3-azure python3-azure-storage python3-babel python3-bcrypt python3-beniget python3-blinker python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cryptography python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-dev python3-distutils python3-dnaio python3-docutils python3-fastjsonschema python3-fonttools python3-frozenlist python3-fs python3-future python3-gast python3-gi python3-git python3-gitdb python3-htseq python3-humanfriendly python3-idna python3-imagesize python3-isodate python3-jinja2 python3-jmespath python3-jsonschema python3-jupyter-core python3-jwt python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-marshmallow python3-matplotlib python3-mdurl python3-minimal python3-mpmath python3-msal python3-msal-extensions python3-msrest python3-msrestazure python3-multidict python3-nacl python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-oauthlib python3-packaging python3-paramiko python3-pbr python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-ply python3-portalocker python3-psutil python3-pulp python3-py python3-py2bit python3-pybigwig python3-pygments python3-pyparsing python3-pyrsistent python3-pysam python3-pythran python3-ratelimiter python3-requests python3-requests-oauthlib python3-retry python3-rich python3-rich-click python3-roman python3-ruamel.yaml python3-ruamel.yaml.clib python3-s3transfer python3-scipy python3-setuptools python3-simplejson python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-strictyaml python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-uamqp python3-ufolib2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yarl python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport 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-blob r-cran-boot r-cran-brio r-cran-broom r-cran-bslib r-cran-cachem r-cran-callr 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-dbi r-cran-desc r-cran-diffobj r-cran-digest 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-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-maptools r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics 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-pkgload r-cran-plogr r-cran-plotly r-cran-plyr r-cran-png r-cran-polynom r-cran-praise r-cran-prettyunits r-cran-proc r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstatix r-cran-sass r-cran-scales r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sp r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat 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-waldo r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xml-core zip zlib1g-dev 0 upgraded, 693 newly installed, 0 to remove and 0 not upgraded. Need to get 642 MB of archives. After this operation, 2947 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 pigz amd64 2.6-1 [64.0 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1+deb12u1 [306 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+deb12u1 [139 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 coinor-libcoinutils3v5 amd64 2.11.4+repack1-2 [440 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 coinor-libosi1v5 amd64 0.108.6+repack1-2 [276 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 coinor-libclp1 amd64 1.17.6-3 [843 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 coinor-libcgl1 amd64 0.60.3+repack1-4 [409 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 coinor-libcbc3 amd64 2.10.8+ds1-1 [715 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 coinor-cbc amd64 2.10.8+ds1-1 [14.8 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1.1 [683 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B] Get:96 http://deb.debian.org/debian bookworm/main amd64 python3-typing-extensions all 4.4.0-1 [45.2 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 python3-xopen all 1.7.0-2 [16.9 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 python3-dnaio amd64 0.10.0-1+b1 [58.4 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 python3-cutadapt amd64 4.2-1+b1 [222 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 cutadapt all 4.2-1 [23.5 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get:103 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1~deb12u1 [43.7 MB] Get:117 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get:118 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:142 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:153 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.11+9-1~deb12u1 [184 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get:173 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libisal2 amd64 2.30.0-5 [107 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 fastp amd64 0.23.2+dfsg-2+b1 [203 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get:180 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6~deb12u1 [154 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-6~deb12u1 [23.5 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-6~deb12u1 [110 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get:196 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libargs4j-java all 2.33-2 [138 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libsis-base-jni amd64 18.09~pre1+git20180928.45fbd31+dfsg-3 [12.5 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libsis-base-java all 18.09~pre1+git20180928.45fbd31+dfsg-3 [97.8 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:214 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 libsis-jhdf5-jni amd64 19.04.1+dfsg-3 [95.9 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 libsis-jhdf5-java all 19.04.1+dfsg-3 [1491 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 fastqc all 0.11.9+dfsg-6 [390 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:226 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB] Get:232 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B] Get:233 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u7 [1899 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB] Get:242 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B] Get:243 http://deb.debian.org/debian bookworm/main amd64 libgirepository-1.0-1 amd64 1.74.0-3 [101 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 gir1.2-glib-2.0 amd64 1.74.0-3 [159 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u6 [385 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 git-man all 1:2.39.2-1.1 [2049 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 git amd64 1:2.39.2-1.1 [7171 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 hisat2 amd64 2.2.1-4+b2 [3658 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 javascript-common all 11+nmu1 [6260 B] Get:251 http://deb.debian.org/debian bookworm/main amd64 libbigwig0 amd64 0.4.7+dfsg-3 [27.9 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:254 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-21 [240 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 libjemalloc2 amd64 5.3.0-1 [275 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get:274 http://deb.debian.org/debian bookworm/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:276 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 libjs-modernizr all 2.6.2+ds1-5 [47.1 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 liblua5.3-0 amd64 5.3.6-2 [123 kB] Get:289 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 libnlopt0 amd64 2.7.1-5 [174 kB] Get:291 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:295 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:296 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:297 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6+deb12u2 [1987 kB] Get:298 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:299 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6+deb12u2 [4742 kB] Get:300 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get:301 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get:302 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get:303 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:304 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:305 http://deb.debian.org/debian bookworm/main amd64 libsodium23 amd64 1.0.18-1 [161 kB] Get:306 http://deb.debian.org/debian bookworm/main amd64 libstaden-read14 amd64 1.14.15-1 [265 kB] Get:307 http://deb.debian.org/debian bookworm/main amd64 libtbbmalloc2 amd64 2021.8.0-2 [46.3 kB] Get:308 http://deb.debian.org/debian bookworm/main amd64 libtbbbind-2-5 amd64 2021.8.0-2 [13.5 kB] Get:309 http://deb.debian.org/debian bookworm/main amd64 libtbb12 amd64 2021.8.0-2 [79.1 kB] Get:310 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1+deb12u1 [136 kB] Get:311 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:312 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:313 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get:314 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:315 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:316 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:317 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:318 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:319 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:320 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:321 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:322 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:323 http://deb.debian.org/debian bookworm/main amd64 megadepth amd64 1.2.0-4 [80.2 kB] Get:324 http://deb.debian.org/debian bookworm/main amd64 python3-colorama all 0.4.6-2 [36.8 kB] Get:325 http://deb.debian.org/debian bookworm/main amd64 python3-click all 8.1.3-2 [92.2 kB] Get:326 http://deb.debian.org/debian bookworm/main amd64 python3-humanfriendly all 10.0-3 [85.2 kB] Get:327 http://deb.debian.org/debian bookworm/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get:328 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:329 http://deb.debian.org/debian bookworm/main amd64 python3-future all 0.18.2-6 [348 kB] Get:330 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get:331 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get:332 http://deb.debian.org/debian bookworm/main amd64 python3-lzstring all 1.0.4-2 [5604 B] Get:333 http://deb.debian.org/debian bookworm/main amd64 python3-markdown all 3.4.1-2 [64.7 kB] Get:334 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get:335 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:336 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:337 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB] Get:338 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get:339 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+deb12u1 [74.2 kB] Get:340 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get:341 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:342 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get:343 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get:344 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get:345 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:346 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:347 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get:348 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6+deb12u2 [615 kB] Get:349 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get:350 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get:351 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:352 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:353 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get:354 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:355 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get:356 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get:357 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get:358 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get:359 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get:360 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:361 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:362 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get:363 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get:364 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get:365 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get:366 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get:367 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get:368 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:369 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get:370 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:371 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:372 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get:373 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1+deb12u1 [41.0 kB] Get:374 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get:375 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get:376 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get:377 http://deb.debian.org/debian bookworm/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get:378 http://deb.debian.org/debian bookworm/main amd64 python3-markdown-it all 2.1.0-5 [58.8 kB] Get:379 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get:380 http://deb.debian.org/debian bookworm/main amd64 python3-rich all 13.3.1-1 [202 kB] Get:381 http://deb.debian.org/debian bookworm/main amd64 python3-rich-click all 1.6.0-1 [20.8 kB] Get:382 http://deb.debian.org/debian bookworm/main amd64 python3-simplejson amd64 3.18.3-1 [59.8 kB] Get:383 http://deb.debian.org/debian bookworm/main amd64 python3-colormath all 3.0.0-4 [34.7 kB] Get:384 http://deb.debian.org/debian bookworm/main amd64 python3-spectra all 0.0.11-4 [16.5 kB] Get:385 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get:386 http://deb.debian.org/debian bookworm/main amd64 multiqc all 1.14+dfsg-1 [657 kB] Get:387 http://deb.debian.org/debian bookworm/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:388 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:389 http://deb.debian.org/debian bookworm/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:390 http://deb.debian.org/debian bookworm/main amd64 pandoc-data all 2.17.1.1-2~deb12u1 [418 kB] Get:391 http://deb.debian.org/debian bookworm/main amd64 pandoc amd64 2.17.1.1-2~deb12u1 [21.3 MB] Get:392 http://deb.debian.org/debian bookworm/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b6 [51.1 kB] Get:393 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get:394 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get:395 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get:396 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get:397 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get:398 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get:399 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get:400 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get:401 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get:402 http://deb.debian.org/debian bookworm/main amd64 python3-numpydoc all 1.5.0-1 [43.0 kB] Get:403 http://deb.debian.org/debian bookworm/main amd64 python3-fastjsonschema all 2.16.3-2 [21.6 kB] Get:404 http://deb.debian.org/debian bookworm/main amd64 python3-pyrsistent amd64 0.18.1-1+b3 [60.0 kB] Get:405 http://deb.debian.org/debian bookworm/main amd64 python3-jsonschema all 4.10.3-1 [67.9 kB] Get:406 http://deb.debian.org/debian bookworm/main amd64 python3-traitlets all 5.5.0-1 [92.4 kB] Get:407 http://deb.debian.org/debian bookworm/main amd64 python3-jupyter-core all 4.12.0-1 [27.3 kB] Get:408 http://deb.debian.org/debian bookworm/main amd64 python3-nbformat all 5.5.0-1 [43.2 kB] Get:409 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get:410 http://deb.debian.org/debian bookworm/main amd64 python3-pbr all 5.10.0-2 [61.4 kB] Get:411 http://deb.debian.org/debian bookworm/main amd64 python3-tenacity all 8.2.1-1 [43.6 kB] Get:412 http://deb.debian.org/debian bookworm/main amd64 python3-plotly all 5.4.1+dfsg-1 [2613 kB] Get:413 http://deb.debian.org/debian bookworm/main amd64 python3-py2bit amd64 0.3.1-1+b2 [18.7 kB] Get:414 http://deb.debian.org/debian bookworm/main amd64 python3-pybigwig amd64 0.3.18+dfsg-1+b3 [34.8 kB] Get:415 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:416 http://deb.debian.org/debian bookworm/main amd64 python3-deeptools all 3.5.1-3 [159 kB] Get:417 http://deb.debian.org/debian bookworm/main amd64 python3-htseq amd64 1.99.2-1+b3 [268 kB] Get:418 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:419 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:420 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:421 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:422 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:423 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:424 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:425 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:426 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:427 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:428 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:429 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:430 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:431 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:432 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:433 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:434 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:435 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:436 http://deb.debian.org/debian bookworm/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:437 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:438 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:439 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:440 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:441 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:442 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:443 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:444 http://deb.debian.org/debian bookworm/main amd64 r-cran-locfit amd64 1.5-9.7-1 [507 kB] Get:445 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:446 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:447 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:448 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:449 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:450 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:451 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:452 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:453 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:454 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:455 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:456 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:457 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:458 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:459 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:460 http://deb.debian.org/debian bookworm/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:461 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:462 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:463 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:464 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:465 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:466 http://deb.debian.org/debian bookworm/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:467 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:468 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:469 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:470 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:471 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:472 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:473 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:474 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:475 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:476 http://deb.debian.org/debian bookworm/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:477 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotate all 1.76.0+dfsg-1 [1727 kB] Get:478 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:479 http://deb.debian.org/debian bookworm/main amd64 r-bioc-geneplotter all 1.76.0-1 [1488 kB] Get:480 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:481 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:482 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:483 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:484 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:485 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:486 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:487 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:488 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:489 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:490 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:491 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:492 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:493 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:494 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:495 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:496 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:497 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:498 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpparmadillo amd64 0.12.0.1.0-1 [841 kB] Get:499 http://deb.debian.org/debian bookworm/main amd64 r-bioc-deseq2 amd64 1.38.3+dfsg-1 [1288 kB] Get:500 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:501 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:502 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:503 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:504 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:505 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:506 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:507 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:508 http://deb.debian.org/debian bookworm/main amd64 r-bioc-tximport all 1.26.1+dfsg-1 [87.9 kB] Get:509 http://deb.debian.org/debian bookworm/main amd64 r-cran-corrplot all 0.92-1 [131 kB] Get:510 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:511 http://deb.debian.org/debian bookworm/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:512 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:513 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmltools amd64 0.5.4-1 [364 kB] Get:514 http://deb.debian.org/debian bookworm/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get:515 http://deb.debian.org/debian bookworm/main amd64 r-cran-later amd64 1.3.0+dfsg-1+b1 [117 kB] Get:516 http://deb.debian.org/debian bookworm/main amd64 r-cran-promises amd64 1.2.0.1+dfsg-1 [274 kB] Get:517 http://deb.debian.org/debian bookworm/main amd64 r-cran-httpuv amd64 1.6.9+dfsg-1 [478 kB] Get:518 http://deb.debian.org/debian bookworm/main amd64 r-cran-fontawesome all 0.5.0-1 [1304 kB] Get:519 http://deb.debian.org/debian bookworm/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:520 http://deb.debian.org/debian bookworm/main amd64 r-cran-commonmark amd64 1.8.1-1 [117 kB] Get:521 http://deb.debian.org/debian bookworm/main amd64 r-cran-fs amd64 1.6.1+dfsg-1 [226 kB] Get:522 http://deb.debian.org/debian bookworm/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:523 http://deb.debian.org/debian bookworm/main amd64 r-cran-sass amd64 0.4.5+dfsg-1 [942 kB] Get:524 http://deb.debian.org/debian bookworm/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:525 http://deb.debian.org/debian bookworm/main amd64 r-cran-bslib all 0.4.2+dfsg-1 [3773 kB] Get:526 http://deb.debian.org/debian bookworm/main amd64 r-cran-shiny all 1.7.4+dfsg-2+deb12u1 [2751 kB] Get:527 http://deb.debian.org/debian bookworm/main amd64 r-cran-crosstalk all 1.2.0+dfsg-1 [171 kB] Get:528 http://deb.debian.org/debian bookworm/main amd64 r-cran-data.table amd64 1.14.8+dfsg-1 [1683 kB] Get:529 http://deb.debian.org/debian bookworm/main amd64 r-cran-evaluate all 0.20-1 [85.9 kB] Get:530 http://deb.debian.org/debian bookworm/main amd64 r-cran-xfun amd64 0.37+dfsg-1 [394 kB] Get:531 http://deb.debian.org/debian bookworm/main amd64 r-cran-highr all 0.10+dfsg-1 [38.1 kB] Get:532 http://deb.debian.org/debian bookworm/main amd64 r-cran-knitr all 1.42+dfsg-1 [901 kB] Get:533 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:534 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:535 http://deb.debian.org/debian bookworm/main amd64 r-cran-tinytex all 0.44-1 [138 kB] Get:536 http://deb.debian.org/debian bookworm/main amd64 r-cran-rmarkdown all 2.20+dfsg-1 [2265 kB] Get:537 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmlwidgets all 1.6.1+dfsg-1 [120 kB] Get:538 http://deb.debian.org/debian bookworm/main amd64 r-cran-dt all 0.27+dfsg-1 [236 kB] Get:539 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggrepel amd64 0.9.3-1 [247 kB] Get:540 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggsci all 2.9-3 [2905 kB] Get:541 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:542 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:543 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:544 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:545 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyr amd64 1.3.0-1 [1183 kB] Get:546 http://deb.debian.org/debian bookworm/main amd64 r-cran-cowplot all 1.1.1+dfsg-1 [636 kB] Get:547 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggsignif all 0.6.4-1 [589 kB] Get:548 http://deb.debian.org/debian bookworm/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:549 http://deb.debian.org/debian bookworm/main amd64 r-cran-polynom all 1.4-1+dfsg-1 [92.5 kB] Get:550 http://deb.debian.org/debian bookworm/main amd64 r-cran-backports amd64 1.4.1-1 [101 kB] Get:551 http://deb.debian.org/debian bookworm/main amd64 r-cran-broom all 1.0.3+dfsg-2 [1776 kB] Get:552 http://deb.debian.org/debian bookworm/main amd64 r-cran-cardata all 3.0.5-1 [1797 kB] Get:553 http://deb.debian.org/debian bookworm/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:554 http://deb.debian.org/debian bookworm/main amd64 r-cran-nnet amd64 7.3-18-1 [112 kB] Get:555 http://deb.debian.org/debian bookworm/main amd64 r-cran-boot all 1.3-28.1-1 [620 kB] Get:556 http://deb.debian.org/debian bookworm/main amd64 r-cran-minqa amd64 1.2.5-1 [113 kB] Get:557 http://deb.debian.org/debian bookworm/main amd64 r-cran-brio amd64 1.1.3-1+b1 [35.5 kB] Get:558 http://deb.debian.org/debian bookworm/main amd64 r-cran-ps amd64 1.7.2-1 [308 kB] Get:559 http://deb.debian.org/debian bookworm/main amd64 r-cran-processx amd64 3.8.0-1 [339 kB] Get:560 http://deb.debian.org/debian bookworm/main amd64 r-cran-callr all 3.7.3-2 [426 kB] Get:561 http://deb.debian.org/debian bookworm/main amd64 r-cran-rprojroot all 2.0.3-1 [119 kB] Get:562 http://deb.debian.org/debian bookworm/main amd64 r-cran-desc all 1.4.2-1 [348 kB] Get:563 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgload all 1.3.2-1 [206 kB] Get:564 http://deb.debian.org/debian bookworm/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:565 http://deb.debian.org/debian bookworm/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB] Get:566 http://deb.debian.org/debian bookworm/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:567 http://deb.debian.org/debian bookworm/main amd64 r-cran-waldo all 0.4.0-1 [116 kB] Get:568 http://deb.debian.org/debian bookworm/main amd64 r-cran-testthat amd64 3.1.6-1 [1545 kB] Get:569 http://deb.debian.org/debian bookworm/main amd64 r-cran-nloptr amd64 2.0.3-1 [375 kB] Get:570 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcppeigen amd64 0.3.3.9.3-1 [1191 kB] Get:571 http://deb.debian.org/debian bookworm/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:572 http://deb.debian.org/debian bookworm/main amd64 r-cran-lme4 amd64 1.1-31-1 [4087 kB] Get:573 http://deb.debian.org/debian bookworm/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] Get:574 http://deb.debian.org/debian bookworm/main amd64 r-cran-pbkrtest all 0.5.2-2 [184 kB] Get:575 http://deb.debian.org/debian bookworm/main amd64 r-cran-sparsem amd64 1.81-1 [905 kB] Get:576 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixmodels all 0.5-1-1 [375 kB] Get:577 http://deb.debian.org/debian bookworm/main amd64 r-cran-survival amd64 3.5-3-1 [5910 kB] Get:578 http://deb.debian.org/debian bookworm/main amd64 r-cran-class amd64 7.3-21-1 [86.7 kB] Get:579 http://deb.debian.org/debian bookworm/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] Get:580 http://deb.debian.org/debian bookworm/main amd64 r-cran-e1071 amd64 1.7-13-1 [568 kB] Get:581 http://deb.debian.org/debian bookworm/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:582 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:583 http://deb.debian.org/debian bookworm/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB] Get:584 http://deb.debian.org/debian bookworm/main amd64 r-cran-plyr amd64 1.8.8-1 [832 kB] Get:585 http://deb.debian.org/debian bookworm/main amd64 r-cran-proc amd64 1.18.0-1+b1 [983 kB] Get:586 http://deb.debian.org/debian bookworm/main amd64 r-cran-tzdb amd64 0.3.0-1 [484 kB] Get:587 http://deb.debian.org/debian bookworm/main amd64 r-cran-clock amd64 0.6.1-2 [1768 kB] Get:588 http://deb.debian.org/debian bookworm/main amd64 r-cran-gower amd64 1.0.1-1 [207 kB] Get:589 http://deb.debian.org/debian bookworm/main amd64 r-cran-hardhat all 1.2.0+dfsg-1 [622 kB] Get:590 http://deb.debian.org/debian bookworm/main amd64 r-cran-rpart amd64 4.1.19-1 [917 kB] Get:591 http://deb.debian.org/debian bookworm/main amd64 r-cran-kernsmooth amd64 2.23-20-1 [91.5 kB] Get:592 http://deb.debian.org/debian bookworm/main amd64 r-cran-globals all 0.16.2-1 [118 kB] Get:593 http://deb.debian.org/debian bookworm/main amd64 r-cran-listenv all 0.9.0+dfsg-1 [112 kB] Get:594 http://deb.debian.org/debian bookworm/main amd64 r-cran-parallelly all 1.34.0-1 [337 kB] Get:595 http://deb.debian.org/debian bookworm/main amd64 r-cran-future all 1.31.0+dfsg-1 [612 kB] Get:596 http://deb.debian.org/debian bookworm/main amd64 r-cran-future.apply all 1.10.0+dfsg-1 [165 kB] Get:597 http://deb.debian.org/debian bookworm/main amd64 r-cran-progressr all 0.13.0-1 [336 kB] Get:598 http://deb.debian.org/debian bookworm/main amd64 r-cran-squarem all 2021.1-1 [179 kB] Get:599 http://deb.debian.org/debian bookworm/main amd64 r-cran-lava all 1.7.2.1+dfsg-1 [2203 kB] Get:600 http://deb.debian.org/debian bookworm/main amd64 r-cran-prodlim amd64 2019.11.13-1+b1 [395 kB] Get:601 http://deb.debian.org/debian bookworm/main amd64 r-cran-ipred amd64 0.9-13-1 [386 kB] Get:602 http://deb.debian.org/debian bookworm/main amd64 r-cran-timechange amd64 0.2.0-1 [178 kB] Get:603 http://deb.debian.org/debian bookworm/main amd64 r-cran-lubridate amd64 1.9.2+dfsg-1 [994 kB] Get:604 http://deb.debian.org/debian bookworm/main amd64 r-cran-timedate amd64 4022.108-1 [1185 kB] Get:605 http://deb.debian.org/debian bookworm/main amd64 r-cran-recipes all 1.0.4+dfsg-1 [1871 kB] Get:606 http://deb.debian.org/debian bookworm/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:607 http://deb.debian.org/debian bookworm/main amd64 r-cran-caret amd64 6.0-93+dfsg-1 [3447 kB] Get:608 http://deb.debian.org/debian bookworm/main amd64 r-cran-conquer amd64 1.3.2-1 [459 kB] Get:609 http://deb.debian.org/debian bookworm/main amd64 r-cran-quantreg amd64 5.94-1 [1535 kB] Get:610 http://deb.debian.org/debian bookworm/main amd64 r-cran-sp amd64 1:1.6-0+dfsg-1 [1532 kB] Get:611 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreign amd64 0.8.84-1 [250 kB] Get:612 http://deb.debian.org/debian bookworm/main amd64 r-cran-maptools amd64 1:1.1-6+dfsg-1 [1558 kB] Get:613 http://deb.debian.org/debian bookworm/main amd64 r-cran-forcats all 1.0.0-1 [413 kB] Get:614 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:615 http://deb.debian.org/debian bookworm/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:616 http://deb.debian.org/debian bookworm/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:617 http://deb.debian.org/debian bookworm/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:618 http://deb.debian.org/debian bookworm/main amd64 r-cran-vroom amd64 1.6.1-1 [842 kB] Get:619 http://deb.debian.org/debian bookworm/main amd64 r-cran-readr amd64 2.1.4-1 [776 kB] Get:620 http://deb.debian.org/debian bookworm/main amd64 r-cran-haven amd64 2.5.1-1 [343 kB] Get:621 http://deb.debian.org/debian bookworm/main amd64 r-cran-rematch all 1.0.1-3 [14.1 kB] Get:622 http://deb.debian.org/debian bookworm/main amd64 r-cran-cellranger all 1.1.0-3 [100 kB] Get:623 http://deb.debian.org/debian bookworm/main amd64 r-cran-readxl amd64 1.4.2-1 [723 kB] Get:624 http://deb.debian.org/debian bookworm/main amd64 r-cran-zip amd64 2.2.2-1+b1 [113 kB] Get:625 http://deb.debian.org/debian bookworm/main amd64 r-cran-openxlsx amd64 4.2.5.2-1 [1929 kB] Get:626 http://deb.debian.org/debian bookworm/main amd64 r-cran-rio all 0.5.29-1 [474 kB] Get:627 http://deb.debian.org/debian bookworm/main amd64 r-cran-car all 3.1-1-1 [1699 kB] Get:628 http://deb.debian.org/debian bookworm/main amd64 r-cran-rstatix all 0.7.2-1 [609 kB] Get:629 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggpubr all 0.6.0-1 [2080 kB] Get:630 http://deb.debian.org/debian bookworm/main amd64 r-cran-miniui all 0.1.1.1-3 [35.9 kB] Get:631 http://deb.debian.org/debian bookworm/main amd64 r-cran-shinyjs all 2.1.0-1 [1009 kB] Get:632 http://deb.debian.org/debian bookworm/main amd64 r-cran-colourpicker all 1.2.0+dfsg-1 [1165 kB] Get:633 http://deb.debian.org/debian bookworm/main amd64 r-cran-plotly all 4.10.1+dfsg-2 [3339 kB] Get:634 http://deb.debian.org/debian bookworm/main amd64 r-cran-gprofiler2 all 0.2.1+dfsg-1 [124 kB] Get:635 http://deb.debian.org/debian bookworm/main amd64 r-cran-pheatmap all 1.0.12-2 [77.9 kB] Get:636 http://deb.debian.org/debian bookworm/main amd64 salmon amd64 1.10.1+ds1-1+b1 [3297 kB] Get:637 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:638 http://deb.debian.org/debian bookworm/main amd64 python3-configargparse all 1.5.3-1 [26.1 kB] Get:639 http://deb.debian.org/debian bookworm/main amd64 python3-connection-pool all 0.0.3-2 [5584 B] Get:640 http://deb.debian.org/debian bookworm/main amd64 python3-datrie amd64 0.8.2-4+b1 [97.7 kB] Get:641 http://deb.debian.org/debian bookworm/main amd64 python3-smmap all 5.0.0-1 [21.0 kB] Get:642 http://deb.debian.org/debian bookworm/main amd64 python3-gitdb all 4.0.9-2 [45.7 kB] Get:643 http://deb.debian.org/debian bookworm/main amd64 python3-git all 3.1.30-1+deb12u2 [135 kB] Get:644 http://deb.debian.org/debian bookworm/main amd64 python3-psutil amd64 5.9.4-1+b1 [189 kB] Get:645 http://deb.debian.org/debian bookworm/main amd64 python3-pulp all 2.6.0+dfsg-1 [66.0 kB] Get:646 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get:647 http://deb.debian.org/debian bookworm/main amd64 python3-retry all 0.9.2-2 [7020 B] Get:648 http://deb.debian.org/debian bookworm/main amd64 python3-isodate all 0.6.1-1 [25.3 kB] Get:649 http://deb.debian.org/debian bookworm/main amd64 python3-blinker all 1.5-1 [14.7 kB] Get:650 http://deb.debian.org/debian bookworm/main amd64 python3-cffi-backend amd64 1.15.1-5+b1 [84.6 kB] Get:651 http://deb.debian.org/debian bookworm/main amd64 python3-cryptography amd64 38.0.4-3 [666 kB] Get:652 http://deb.debian.org/debian bookworm/main amd64 python3-jwt all 2.6.0-1 [26.6 kB] Get:653 http://deb.debian.org/debian bookworm/main amd64 python3-oauthlib all 3.2.2-1 [95.4 kB] Get:654 http://deb.debian.org/debian bookworm/main amd64 python3-requests-oauthlib all 1.3.0+ds-1 [20.7 kB] Get:655 http://deb.debian.org/debian bookworm/main amd64 python3-msrest all 0.6.21-2 [48.0 kB] Get:656 http://deb.debian.org/debian bookworm/main amd64 python3-adal all 1.2.7-2 [32.1 kB] Get:657 http://deb.debian.org/debian bookworm/main amd64 python3-msrestazure all 0.6.4-2 [26.4 kB] Get:658 http://deb.debian.org/debian bookworm/main amd64 python3-avro all 1.11.1+dfsg-2 [70.5 kB] Get:659 http://deb.debian.org/debian bookworm/main amd64 python3-multidict amd64 6.0.4-1+b1 [31.6 kB] Get:660 http://deb.debian.org/debian bookworm/main amd64 python3-yarl amd64 1.8.2-1+b1 [49.8 kB] Get:661 http://deb.debian.org/debian bookworm/main amd64 python3-async-timeout all 4.0.2-1 [7476 B] Get:662 http://deb.debian.org/debian bookworm/main amd64 python3-frozenlist amd64 1.3.3-1+b1 [30.0 kB] Get:663 http://deb.debian.org/debian bookworm/main amd64 python3-aiosignal all 1.3.1-1 [6016 B] Get:664 http://deb.debian.org/debian bookworm/main amd64 python3-aiohttp amd64 3.8.4-1 [251 kB] Get:665 http://deb.debian.org/debian bookworm/main amd64 python3-azure-storage all 20230112+git-1 [280 kB] Get:666 http://deb.debian.org/debian bookworm/main amd64 python3-marshmallow all 3.18.0-1 [66.3 kB] Get:667 http://deb.debian.org/debian bookworm/main amd64 python3-msal all 1.21.0-1 [85.9 kB] Get:668 http://deb.debian.org/debian bookworm/main amd64 python3-gi amd64 3.42.2-3+b1 [219 kB] Get:669 http://deb.debian.org/debian bookworm/main amd64 python3-portalocker all 2.2.1-1 [18.5 kB] Get:670 http://deb.debian.org/debian bookworm/main amd64 python3-msal-extensions all 1.0.0-2 [16.9 kB] Get:671 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml.clib amd64 0.2.7-1+b2 [113 kB] Get:672 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get:673 http://deb.debian.org/debian bookworm/main amd64 python3-strictyaml all 1.6.1-3 [92.9 kB] Get:674 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB] Get:675 http://deb.debian.org/debian bookworm/main amd64 python3-uamqp amd64 1.5.3-1+b4 [647 kB] Get:676 http://deb.debian.org/debian bookworm/main amd64 python3-azure all 20230112+git-1 [11.9 MB] Get:677 http://deb.debian.org/debian bookworm/main amd64 python3-jmespath all 1.0.1-1 [21.1 kB] Get:678 http://deb.debian.org/debian bookworm/main amd64 python3-botocore all 1.29.27+repack-1 [5502 kB] Get:679 http://deb.debian.org/debian bookworm/main amd64 python3-s3transfer all 0.6.0-1 [53.0 kB] Get:680 http://deb.debian.org/debian bookworm/main amd64 python3-boto3 all 1.26.27+dfsg-1 [187 kB] Get:681 http://deb.debian.org/debian bookworm/main amd64 python3-bcrypt amd64 3.2.2-1 [32.2 kB] Get:682 http://deb.debian.org/debian bookworm/main amd64 python3-nacl amd64 1.5.0-2 [59.3 kB] Get:683 http://deb.debian.org/debian bookworm/main amd64 python3-paramiko all 2.12.0-2 [133 kB] Get:684 http://deb.debian.org/debian bookworm/main amd64 python3-smart-open all 5.2.1-5 [87.9 kB] Get:685 http://deb.debian.org/debian bookworm/main amd64 python3-stopit all 1.1.2-2 [12.6 kB] Get:686 http://deb.debian.org/debian bookworm/main amd64 python3-tabulate all 0.8.9-1 [35.2 kB] Get:687 http://deb.debian.org/debian bookworm/main amd64 python3-throttler all 1.2.2-2 [7072 B] Get:688 http://deb.debian.org/debian bookworm/main amd64 python3-toposort all 1.9-1 [7272 B] Get:689 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.14.1-2+b2 [42.1 kB] Get:690 http://deb.debian.org/debian bookworm/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B] Get:691 http://deb.debian.org/debian bookworm/main amd64 snakemake all 7.21.0-1 [301 kB] Get:692 http://deb.debian.org/debian bookworm/main amd64 trim-galore all 0.6.10-1 [17.8 MB] Get:693 http://deb.debian.org/debian bookworm/main amd64 pigx-rnaseq all 0.1.0-1.1 [61.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 642 MB in 43s (14.8 MB/s) Selecting previously unselected package perl-modules-5.36. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6093 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../3-libperl5.36_5.36.0-7+deb12u1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7+deb12u1) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl (5.36.0-7+deb12u1) ... Selecting previously unselected package pigz. Preparing to unpack .../5-pigz_2.6-1_amd64.deb ... Unpacking pigz (2.6-1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../6-libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../7-libpython3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../8-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../9-python3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6+deb12u2) ... Setting up libssl3:amd64 (3.0.13-1~deb12u1) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6+deb12u2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8434 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../02-libncursesw6_6.4-4_amd64.deb ... Unpacking libncursesw6:amd64 (6.4-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../03-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../04-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../05-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../06-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../07-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... 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Preparing to unpack .../664-trim-galore_0.6.10-1_all.deb ... Unpacking trim-galore (0.6.10-1) ... Selecting previously unselected package pigx-rnaseq. Preparing to unpack .../665-pigx-rnaseq_0.1.0-1.1_all.deb ... Unpacking pigx-rnaseq (0.1.0-1.1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libjs-json (0~20221030+~1.0.8-1) ... Setting up javascript-common (11+nmu1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libtbbmalloc2:amd64 (2021.8.0-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libsodium23:amd64 (1.0.18-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up java-common (0.74) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libjs-popper.js (1.16.1+ds-6) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up libjs-sifter.js (0.6.0+dfsg-3) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libglvnd0:amd64 (1.6.0-1) ... Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libmjson-java (1.4.0-3) ... Setting up fonts-lyx (2.3.7-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libisal2 (2.30.0-5) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-1+deb12u1) ... Setting up binutils-common:amd64 (2.40-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up node-html5shiv (3.7.3+dfsg-5) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up linux-libc-dev:amd64 (6.1.94-1) ... Setting up libctf-nobfd0:amd64 (2.40-2) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libnlopt0:amd64 (2.7.1-5) ... Setting up libjs-microplugin.js (0.0.3+dfsg-1.1) ... Setting up libjemalloc2:amd64 (5.3.0-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjs-modernizr (2.6.2+ds1-5) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libjansson4:amd64 (2.14-2) ... Setting up libsnappy1v5:amd64 (1.1.9-3) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libjs-es5-shim (4.6.7-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up fastp (0.23.2+dfsg-2+b1) ... Setting up libasound2-data (1.2.8-1) ... Setting up libsis-base-jni (18.09~pre1+git20180928.45fbd31+dfsg-3) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up zip (3.0-13) ... Setting up librhino-java (1.7.14-2.1) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libuv1:amd64 (1.44.2-1+deb12u1) ... Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libmpfr6:amd64 (4.2.0-1) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libjs-d3 (3.5.17-4) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libmpc3:amd64 (1.3.1-1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up pigz (2.6-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up liblua5.3-0:amd64 (5.3.6-2) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up git-man (1:2.39.2-1.1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libgirepository-1.0-1:amd64 (1.74.0-3) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up node-bootstrap-sass (3.4.3-2) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.31) ... Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... Setting up pandoc-data (2.17.1.1-2~deb12u1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.40-2) ... Setting up libisl23:amd64 (0.25-1.1) ... Setting up libc-dev-bin (2.36-9+deb12u7) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up node-normalize.css (8.0.1-5) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libcc1-0:amd64 (12.2.0-14) ... Setting up libargs4j-java (2.33-2) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libgdbm6:amd64 (1.23-3) ... 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 libctf0:amd64 (2.40-2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up cpp-12 (12.2.0-14) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libtbbbind-2-5:amd64 (2021.8.0-2) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.4+repack1-2) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgprofng0:amd64 (2.40-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-2~deb12u1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up shared-mime-info (2.2-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up ucf (3.0043+nmu1) ... Setting up gir1.2-glib-2.0:amd64 (1.74.0-3) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up coinor-libosi1v5:amd64 (0.108.6+repack1-2) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up cpp (4:12.2.0-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u6) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+deb12u1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up ca-certificates-java (20230710~deb12u1) ... No JRE found. Skipping Java certificates setup. Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up binutils-x86-64-linux-gnu (2.40-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u6) ... Setting up libtbb12:amd64 (2021.8.0-2) ... Setting up libbigwig0:amd64 (0.4.7+dfsg-3) ... Setting up binutils (2.40-2) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up adwaita-icon-theme (43-1) ... 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 gcc-12 (12.2.0-14) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up coinor-libclp1:amd64 (1.17.6-3) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-3) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libsis-jhdf5-jni (19.04.1+dfsg-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up coinor-libcgl1:amd64 (0.60.3+repack1-4) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libstaden-read14:amd64 (1.14.15-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up coinor-libcbc3:amd64 (2.10.8+ds1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libsis-jhdf5-java (19.04.1+dfsg-3) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up libfindbin-libs-perl (3.0.2-1) ... Setting up gcc (4:12.2.0-3) ... Setting up samtools (1.16.1-1) ... Setting up liberror-perl (0.17029-2) ... Setting up salmon (1.10.1+ds1-1+b1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up coinor-cbc (2.10.8+ds1-1) ... Setting up sphinx-common (5.3.0-4) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-squarem (2021.1-1) ... Setting up megadepth (1.2.0-4) ... Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up git (1:2.39.2-1.1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-ps (1.7.2-1) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up r-cran-formatr (1.14-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up r-cran-zip (2.2.2-1+b1) ... Setting up r-cran-xml (3.99-0.13-1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up r-cran-locfit (1.5-9.7-1) ... Setting up r-cran-sparsem (1.81-1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up libc6-dev:amd64 (2.36-9+deb12u7) ... Setting up r-cran-nnet (7.3-18-1) ... 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 (1.8.1-1) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... 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 (1.2.9-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up r-cran-fs (1.6.1+dfsg-1) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up r-cran-curl (5.0.0+dfsg-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-cran-brio (1.1.3-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up r-cran-boot (1.3-28.1-1) ... Setting up r-cran-diffobj (0.3.5-1+b1) ... Setting up r-cran-rematch (1.0.1-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up r-cran-matrixstats (0.63.0-1) ... Setting up r-cran-listenv (0.9.0+dfsg-1) ... Setting up littler (0.3.17-1) ... Setting up libpython3.11:amd64 (3.11.2-6+deb12u2) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up r-cran-xfun (0.37+dfsg-1) ... Setting up r-cran-sys (3.4.1-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-backports (1.4.1-1) ... Setting up r-cran-processx (3.8.0-1) ... Setting up r-cran-mime (0.12-1+b1) ... Setting up r-cran-praise (1.0.0-4) ... 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 (1.4-5-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up r-cran-digest (0.6.31-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up r-cran-yaml (2.3.7-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-gower (1.0.1-1) ... Setting up r-cran-evaluate (0.20-1) ... Setting up r-cran-dbi (1.1.3-1) ... Setting up r-cran-timedate (4022.108-1) ... Setting up r-cran-highr (0.10+dfsg-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-cardata (3.0.5-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up python3 (3.11.2-1+b1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-data.table (1.14.8+dfsg-1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-foreign (0.8.84-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-bitops (1.0-7-1) ... Setting up python3-psutil (5.9.4-1+b1) ... Setting up r-cran-rprojroot (2.0.3-1) ... Setting up python3-multidict (6.0.4-1+b1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up python3-tz (2022.7.1-4) ... Setting up r-cran-progressr (0.13.0-1) ... Setting up python3-frozenlist (1.3.3-1+b1) ... Setting up python3-aiosignal (1.3.1-1) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up python3-async-timeout (4.0.2-1) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.1-1) ... Setting up r-cran-png (0.1-8-1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-simplejson (3.18.3-1) ... Setting up r-bioc-biobase (2.58.0-2) ... Setting up r-cran-jsonlite (1.8.4+dfsg-1) ... Setting up python3-isodate (0.6.1-1) ... Setting up r-cran-corrplot (0.92-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up r-cran-sp (1:1.6-0+dfsg-1) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up python3-packaging (23.0-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-parallelly (1.34.0-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up r-cran-stringi (1.7.12-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-humanfriendly (10.0-3) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-avro (1.11.1+dfsg-2) ... Setting up r-cran-cpp11 (0.4.3-1) ... Setting up python3-jmespath (1.0.1-1) ... Setting up r-cran-plyr (1.8.8-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up python3-mdurl (0.1.2-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up python3-gi (3.42.2-3+b1) ... Setting up python3-cycler (0.11.0-1) ... Setting up r-cran-gridextra (2.3-3) ... Setting up python3-connection-pool (0.0.3-2) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1+deb12u1) ... Setting up python3-wrapt (1.14.1-2+b2) ... Setting up python3-markdown (3.4.1-2) ... Setting up python3-throttler (1.2.2-2) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up r-cran-later (1.3.0+dfsg-1+b1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up r-cran-tinytex (0.44-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up r-bioc-tximport (1.26.1+dfsg-1) ... Setting up python3-markdown-it (2.1.0-5) ... Setting up r-cran-kernsmooth (2.23-20-1) ... Setting up r-cran-knitr (1.42+dfsg-1) ... Setting up python3-fastjsonschema (2.16.3-2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up python3-pyrsistent:amd64 (0.18.1-1+b3) ... Setting up hisat2 (2.2.1-4+b2) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-portalocker (2.2.1-1) ... Setting up r-cran-cachem (1.0.7-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-py2bit (0.3.1-1+b2) ... Setting up r-cran-rcpparmadillo (0.12.0.1.0-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up python3-datrie:amd64 (0.8.2-4+b1) ... Setting up r-cran-rjson (0.2.21-1) ... Setting up r-cran-tzdb (0.3.0-1) ... Setting up python3-mpmath (1.2.1-2) ... Setting up r-cran-globals (0.16.2-1) ... Setting up r-cran-rcurl (1.98-1.10+dfsg-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up r-cran-maptools (1:1.1-6+dfsg-1) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-yarl (1.8.2-1+b1) ... Setting up python3-smmap (5.0.0-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up python3-cffi-backend:amd64 (1.15.1-5+b1) ... Setting up r-cran-rcppeigen (0.3.3.9.3-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up g++-12 (12.2.0-14) ... Setting up python3-blinker (1.5-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-toposort (1.9-1) ... Setting up python3-configargparse (1.5.3-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up r-cran-minqa (1.2.5-1) ... Setting up python3-attr (22.2.0-1) ... Setting up r-cran-openssl (2.0.5+dfsg-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up r-cran-stringr (1.5.0-1) ... Setting up r-cran-class (7.3-21-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up r-cran-callr (3.7.3-2) ... Setting up r-cran-openxlsx (4.2.5.2-1) ... Setting up python3-jwt (2.6.0-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-deeptoolsintervals (0.1.9-3+b6) ... Setting up python3-colorama (0.4.6-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-pbr (5.10.0-2) ... Setting up python3-pulp (2.6.0+dfsg-1) ... Setting up r-cran-matrixmodels (0.5-1-1) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up r-cran-desc (1.4.2-1) ... Setting up python3-tenacity (8.2.1-1) ... Setting up python3-bcrypt (3.2.2-1) ... Setting up python3-ply (3.11-5) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.7-1+b2) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up python3-gast (0.5.2-2) ... Setting up r-cran-clock (0.6.1-2) ... Setting up python3-aiohttp (3.8.4-1) ... Setting up python3-marshmallow (3.18.0-1) ... Setting up r-cran-proc (1.18.0-1+b1) ... Setting up python3-tabulate (0.8.9-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up r-cran-survival (3.5-3-1) ... Setting up r-bioc-biocio (1.8.0+dfsg-1) ... Setting up python3-gitdb (4.0.9-2) ... Setting up python3-uamqp (1.5.3-1+b4) ... Setting up python3-click (8.1.3-2) ... Setting up python3-networkx (2.8.8-1) ... Setting up r-cran-future (1.31.0+dfsg-1) ... Setting up r-cran-forcats (1.0.0-1) ... Setting up r-bioc-zlibbioc (1.44.0+dfsg-1) ... Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up python3-fs (2.4.16-2) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up r-cran-future.apply (1.10.0+dfsg-1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-timechange (0.2.0-1) ... Setting up python3-jsonschema (4.10.3-1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up python3-cryptography (38.0.4-3) ... Setting up python3-git (3.1.30-1+deb12u2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-lava (1.7.2.1+dfsg-1) ... Setting up r-cran-promises (1.2.0.1+dfsg-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-e1071 (1.7-13-1) ... Setting up python3-retry (0.9.2-2) ... Setting up r-cran-blob (1.2.3-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up r-cran-htmltools (0.5.4-1) ... Setting up python3-colormath (3.0.0-4) ... Setting up python3-pybigwig (0.3.18+dfsg-1+b3) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up g++ (4:12.2.0-3) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-adal (1.2.7-2) ... Setting up python3-stopit (1.1.2-2) ... Setting up r-cran-hardhat (1.2.0+dfsg-1) ... Setting up r-cran-sass (0.4.5+dfsg-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up python3-future (0.18.2-6) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-lzstring (1.0.4-2) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up python3-htseq (1.99.2-1+b3) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up python3-nacl (1.5.0-2) ... Setting up python3-dnaio (0.10.0-1+b1) ... Setting up r-cran-bh (1.74.0-2) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-lubridate (1.9.2+dfsg-1) ... Setting up r-cran-pkgload (1.3.2-1) ... Setting up r-cran-vroom (1.6.1-1) ... Setting up r-cran-prodlim (2019.11.13-1+b1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up python3-spectra (0.0.11-4) ... Setting up python3-rich (13.3.1-1) ... Setting up python3.11-dev (3.11.2-6+deb12u2) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up r-cran-ggsignif (0.6.4-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-cran-cellranger (1.1.0-3) ... Setting up r-cran-httpuv (1.6.9+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-rpart (4.1.19-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up python3-msal (1.21.0-1) ... Setting up r-cran-fontawesome (0.5.0-1) ... Setting up python3-msal-extensions (1.0.0-2) ... Setting up r-cran-ggsci (2.9-3) ... Setting up python3-nbformat (5.5.0-1) ... Setting up r-cran-ipred (0.9-13-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up python3-strictyaml (1.6.1-3) ... Setting up python3-oauthlib (3.2.2-1) ... Setting up python3-cutadapt (4.2-1+b1) ... Setting up r-cran-bslib (0.4.2+dfsg-1) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up r-cran-readr (2.1.4-1) ... Setting up python3-botocore (1.29.27+repack-1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up r-cran-waldo (0.4.0-1) ... Setting up r-cran-ggrepel (0.9.3-1) ... Setting up r-cran-tidyr (1.3.0-1) ... Setting up python3-plotly (5.4.1+dfsg-1) ... Setting up r-bioc-rsamtools (2.14.0-1) ... Setting up r-cran-recipes (1.0.4+dfsg-1) ... Setting up python3-rich-click (1.6.0-1) ... Setting up python3-paramiko (2.12.0-2) ... Setting up python3-requests-oauthlib (1.3.0+ds-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up r-cran-cowplot (1.1.1+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Setting up r-cran-readxl (1.4.2-1) ... Setting up r-bioc-keggrest (1.38.0+dfsg-1) ... Setting up r-cran-haven (2.5.1-1) ... Setting up cutadapt (4.2-1) ... Setting up r-bioc-annotationdbi (1.60.0-1) ... Setting up python3-s3transfer (0.6.0-1) ... Setting up r-cran-caret (6.0-93+dfsg-1) ... Setting up r-cran-shiny (1.7.4+dfsg-2+deb12u1) ... Setting up r-cran-shinyjs (2.1.0-1) ... Setting up python3-msrest (0.6.21-2) ... Setting up r-cran-testthat (3.1.6-1) ... Setting up r-cran-miniui (0.1.1.1-3) ... Setting up r-cran-broom (1.0.3+dfsg-2) ... Setting up r-bioc-annotate (1.76.0+dfsg-1) ... Setting up r-cran-rmarkdown (2.20+dfsg-1) ... Setting up r-cran-conquer (1.3.2-1) ... Setting up python3-boto3 (1.26.27+dfsg-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up r-bioc-genomicalignments (1.34.0-1) ... Setting up python3-msrestazure (0.6.4-2) ... Setting up r-bioc-geneplotter (1.76.0-1) ... Setting up r-cran-crosstalk (1.2.0+dfsg-1) ... Setting up r-cran-rio (0.5.29-1) ... Setting up r-bioc-rtracklayer (1.58.0-1) ... Setting up r-cran-nloptr (2.0.3-1) ... Setting up python3-scipy (1.10.1-2) ... Setting up r-cran-quantreg (5.94-1) ... Setting up trim-galore (0.6.10-1) ... Setting up r-bioc-deseq2 (1.38.3+dfsg-1) ... Setting up r-cran-lme4 (1.1-31-1) ... Setting up r-cran-htmlwidgets (1.6.1+dfsg-1) ... Setting up r-cran-colourpicker (1.2.0+dfsg-1) ... Setting up r-cran-pbkrtest (0.5.2-2) ... Setting up r-cran-car (3.1-1-1) ... Setting up r-cran-dt (0.27+dfsg-1) ... Setting up r-cran-rstatix (0.7.2-1) ... Setting up r-cran-plotly (4.10.1+dfsg-2) ... Setting up r-cran-ggpubr (0.6.0-1) ... Setting up r-cran-gprofiler2 (0.2.1+dfsg-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-azure (20230112+git-1) ... Setting up python3-azure-storage (20230112+git-1) ... Setting up python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-smart-open (5.2.1-5) ... Setting up multiqc (1.14+dfsg-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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: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:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.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:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up fastqc (0.11.9+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up snakemake (7.21.0-1) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-numpydoc (1.5.0-1) ... Setting up python3-deeptools (3.5.1-3) ... Setting up pigx-rnaseq (0.1.0-1.1) ... Processing triggers for ca-certificates (20230311) ... 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 (20230710~deb12u1) ... done. 4m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 4m46.6s INFO: Running scripts post_install 4m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 4m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 4m46.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 4m51.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 4m52.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpcd0u3cip to bookworm-next 4m52.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 4m52.1s INFO: Running scripts pre_distupgrade 4m52.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 4m52.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 4m52.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_exceptions'] 4m52.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_exceptions'] 4m52.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 4m52.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 4m52.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_zz_database-server'] 4m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_zz_database-server'] 4m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 4m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 4m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'update'] 4m54.1s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [108 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [62.5 kB] Fetched 645 kB in 1s (669 kB/s) Reading package lists... 4m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'update'] 4m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-yf', 'dist-upgrade'] 5m4.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gtk-update-icon-cache libc-bin libc-dev-bin libc6 libc6-dev libcups2 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 linux-libc-dev openjdk-17-jre openjdk-17-jre-headless openssl python3-numpy 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 65.4 MB of archives. After this operation, 1679 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6-dev amd64 2.36-9+deb12u8 [1900 kB] Get:2 http://security.debian.org bookworm-security/main amd64 linux-libc-dev amd64 6.1.99-1 [2007 kB] Get:3 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-dev-bin amd64 2.36-9+deb12u8 [46.3 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:5 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:6 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:7 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:8 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:9 http://security.debian.org bookworm-security/main amd64 openjdk-17-jre amd64 17.0.12+7-2~deb12u1 [184 kB] Get:10 http://security.debian.org bookworm-security/main amd64 openjdk-17-jre-headless amd64 17.0.12+7-2~deb12u1 [43.7 MB] Get:11 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:12 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:13 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:14 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u2 [44.2 kB] Get:15 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] Get:16 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libcups2 amd64 2.4.2-3+deb12u7 [245 kB] Get:17 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libgtk2.0-common all 2.24.33-2+deb12u1 [2660 kB] Get:18 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libgtk2.0-0 amd64 2.24.33-2+deb12u1 [1811 kB] Get:19 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.13-1~deb12u2 [1421 kB] Get:20 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 65.4 MB in 0s (165 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 ... 126815 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.36-9+deb12u8_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../linux-libc-dev_6.1.99-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.99-1) over (6.1.94-1) ... Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 126815 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (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 ... 126815 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 126815 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 126815 files and directories currently installed.) Preparing to unpack .../00-gtk-update-icon-cache_3.24.38-2~deb12u2_amd64.deb ... Unpacking gtk-update-icon-cache (3.24.38-2~deb12u2) over (3.24.38-2~deb12u1) ... Preparing to unpack .../01-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../02-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../03-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../04-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../05-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../06-libcups2_2.4.2-3+deb12u7_amd64.deb ... Unpacking libcups2:amd64 (2.4.2-3+deb12u7) over (2.4.2-3+deb12u5) ... Preparing to unpack .../07-libgtk2.0-common_2.24.33-2+deb12u1_all.deb ... Unpacking libgtk2.0-common (2.24.33-2+deb12u1) over (2.24.33-2) ... Preparing to unpack .../08-libgtk2.0-0_2.24.33-2+deb12u1_amd64.deb ... Unpacking libgtk2.0-0:amd64 (2.24.33-2+deb12u1) over (2.24.33-2) ... Preparing to unpack .../09-openjdk-17-jre_17.0.12+7-2~deb12u1_amd64.deb ... Unpacking openjdk-17-jre:amd64 (17.0.12+7-2~deb12u1) over (17.0.11+9-1~deb12u1) ... Preparing to unpack .../10-openjdk-17-jre-headless_17.0.12+7-2~deb12u1_amd64.deb ... Unpacking openjdk-17-jre-headless:amd64 (17.0.12+7-2~deb12u1) over (17.0.11+9-1~deb12u1) ... Preparing to unpack .../11-openssl_3.0.13-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../12-python3-numpy_1%3a1.24.2-1+deb12u1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1+deb12u1) over (1:1.24.2-1) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u2) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up linux-libc-dev:amd64 (6.1.99-1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up python3-numpy (1:1.24.2-1+deb12u1) ... Setting up libgtk2.0-common (2.24.33-2+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libc-dev-bin (2.36-9+deb12u8) ... Setting up openssl (3.0.13-1~deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up libcups2:amd64 (2.4.2-3+deb12u7) ... Setting up libc6-dev:amd64 (2.36-9+deb12u8) ... Setting up libgtk2.0-0:amd64 (2.24.33-2+deb12u1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.12+7-2~deb12u1) ... Installing new version of config file /etc/java-17-openjdk/jfr/default.jfc ... Installing new version of config file /etc/java-17-openjdk/jfr/profile.jfc ... Installing new version of config file /etc/java-17-openjdk/security/java.security ... Processing triggers for libc-bin (2.36-9+deb12u8) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... done. Setting up openjdk-17-jre:amd64 (17.0.12+7-2~deb12u1) ... 5m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-yf', 'dist-upgrade'] 5m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m5.0s DUMP: 8d734360ea7c957ed98a0e4620f217b3 - 5m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 5m5.3s DUMP: Package: pigx-rnaseq Version: 0.1.0-1.1 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 (>= 0.15+dfsg-2), 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_0.1.0-1.1_all.deb Size: 61244 MD5sum: c498fc408d04299178397f05965119df SHA256: 32b5f61115e9fbe559bf2f2dc316127579029f6a4309457906c100956c9ee553 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'show', '--no-all-versions', 'pigx-rnaseq'] 5m5.3s INFO: apt-cache knows about the following packages: pigx-rnaseq 5m5.3s INFO: Running scripts pre_install 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 5m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 5m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 5m5.5s DUMP: pigx-rnaseq: Installed: 0.1.0-1.1 Candidate: 0.1.0-1.1 Version table: *** 0.1.0-1.1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 5m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 5m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 5m6.1s DUMP: Reading package lists... Building dependency tree... Reading state information... pigx-rnaseq is already the newest version (0.1.0-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq'] 5m6.1s INFO: Running scripts post_install 5m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 5m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 5m6.1s INFO: Running scripts post_distupgrade 5m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_exceptions'] 5m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_exceptions'] 5m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_zz_backports'] 5m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_distupgrade_zz_backports'] 5m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m10.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m16.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m16.1s INFO: Running scripts pre_install 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 5m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_database-server'] 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 5m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_exceptions'] 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 5m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_extras'] 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 5m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture'] 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 5m16.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy'] 5m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 5m16.2s DUMP: pigx-rnaseq: Installed: 0.1.0-1.1 Candidate: 0.1.0-1.1 Version table: *** 0.1.0-1.1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 5m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-cache', 'policy', 'pigx-rnaseq'] 5m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.0-1.1'] 5m16.8s DUMP: Reading package lists... Building dependency tree... Reading state information... pigx-rnaseq is already the newest version (0.1.0-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', '-y', 'install', 'pigx-rnaseq=0.1.0-1.1'] 5m16.8s INFO: Running scripts post_install 5m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 5m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_install_exceptions'] 5m17.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m22.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 5m23.9s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 5m24.2s INFO: /bin converted to /usr/bin by /usr merge 5m24.2s INFO: /lib converted to /usr/lib by /usr merge 5m24.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 5m24.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 5m24.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 5m24.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 5m24.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 5m24.2s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 5m24.2s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 5m24.2s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 5m24.2s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 5m24.2s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 5m24.2s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 5m24.2s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 5m24.2s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 5m24.2s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 5m24.2s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 5m24.2s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 5m24.2s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 5m24.2s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 5m24.2s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 5m24.2s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 5m24.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 5m24.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 5m24.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 5m24.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 5m24.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 5m24.2s INFO: /sbin converted to /usr/sbin by /usr merge 5m32.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', '-ac', '--ignore-obsolete'] 5m46.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', '-ac', '--ignore-obsolete'] 5m46.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m46.8s DUMP: 0.15.6 5m46.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 5m46.8s INFO: Running adequate version 0.15.6 now. 5m46.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'pigx-rnaseq'] 5m46.9s 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 5m46.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'pigx-rnaseq'] 5m46.9s 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 5m46.9s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 5m46.9s INFO: Running scripts pre_remove 5m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 6m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 6m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 6m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 6m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 6m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 6m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_exceptions'] 6m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/pre_remove_exceptions'] 6m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 6m17.9s DUMP: install ok installed adduser adduser 3.134 install ok installed adwaita-icon-theme adwaita-icon-theme 43-1 install ok installed apt apt 2.6.1 install ok installed at-spi2-common at-spi2-common 2.46.0-5 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed binutils binutils 2.40-2 install ok installed binutils-common:amd64 binutils-common 2.40-2 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.40-2 install ok installed blt blt 2.5.3+dfsg-4.1 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed ca-certificates-java ca-certificates-java 20230710~deb12u1 install ok installed coinor-cbc coinor-cbc 2.10.8+ds1-1 install ok installed coinor-libcbc3:amd64 coinor-libcbc3 2.10.8+ds1-1 install ok installed coinor-libcgl1:amd64 coinor-libcgl1 0.60.3+repack1-4 install ok installed coinor-libclp1:amd64 coinor-libclp1 1.17.6-3 install ok installed coinor-libcoinutils3v5:amd64 coinor-libcoinutils3v5 2.11.4+repack1-2 install ok installed coinor-libosi1v5:amd64 coinor-libosi1v5 0.108.6+repack1-2 install ok installed coreutils coreutils 9.1-1 install ok installed cpp cpp 4:12.2.0-3 install ok installed cpp-12 cpp-12 12.2.0-14 install ok installed cutadapt cutadapt 4.2-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed default-jre default-jre 2:1.17-74 install ok installed default-jre-headless default-jre-headless 2:1.17-74 install ok installed diffutils diffutils 1:3.8-4 install ok installed docutils-common docutils-common 0.19+dfsg-6 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed fastp fastp 0.23.2+dfsg-2+b1 install ok installed fastqc fastqc 0.11.9+dfsg-6 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 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 2.3.7-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed g++ g++ 4:12.2.0-3 install ok installed g++-12 g++-12 12.2.0-14 install ok installed gcc gcc 4:12.2.0-3 install ok installed gcc-12 gcc-12 12.2.0-14 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gir1.2-glib-2.0:amd64 gir1.2-glib-2.0 1.74.0-3 install ok installed git git 1:2.39.2-1.1 install ok installed git-man git-man 1:2.39.2-1.1 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.38-2~deb12u2 install ok installed gzip gzip 1.12-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hisat2 hisat2 2.2.1-4+b2 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed java-common java-common 0.74 install ok installed javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libaec0:amd64 libaec0 1.0.6-1+b1 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libargs4j-java libargs4j-java 2.33-2 install ok installed libasan8:amd64 libasan8 12.2.0-14 install ok installed libasound2:amd64 libasound2 1.2.8-1+b1 install ok installed libasound2-data libasound2-data 1.2.8-1 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.46.0-5 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-10 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-10 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-10 install ok installed libbigwig0:amd64 libbigwig0 0.4.7+dfsg-3 install ok installed libbinutils:amd64 libbinutils 2.40-2 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost-filesystem1.74.0:amd64 libboost-filesystem1.74.0 1.74.0+ds1-21 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0+ds1-21 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0+ds1-21 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-21 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc-dev-bin libc-dev-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libc6-dev:amd64 libc6-dev 2.36-9+deb12u8 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcc1-0:amd64 libcc1-0 12.2.0-14 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcommons-compress-java libcommons-compress-java 1.22-1 install ok installed libcommons-io-java libcommons-io-java 2.11.0-2 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.12.0-2 install ok installed libcommons-logging-java libcommons-logging-java 1.2-3 install ok installed libcommons-math3-java libcommons-math3-java 3.6.1-3 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.33-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.40-2 install ok installed libctf0:amd64 libctf0 2.40-2 install ok installed libcups2:amd64 libcups2 2.4.2-3+deb12u7 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.88.1-10+deb12u6 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u6 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-1~deb12u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.114-1+b1 install ok installed libdrm-common libdrm-common 2.4.114-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.114-1+b1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.114-1+b1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.114-1+b1 install ok installed libdrm2:amd64 libdrm2 2.4.114-1+b1 install ok installed libedit2:amd64 libedit2 3.1-20221030-2 install ok installed libelf1:amd64 libelf1 0.188-2.1 install ok installed liberror-perl liberror-perl 0.17029-2 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 3.0.2-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.2.0-14 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-1+deb12u1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-1+deb12u1 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libgif7:amd64 libgif7 5.2.1-2.5 install ok installed libgirepository-1.0-1:amd64 libgirepository-1.0-1 1.74.0-3 install ok installed libgl1:amd64 libgl1 1.6.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 22.3.6-1+deb12u1 install ok installed libglapi-mesa:amd64 libglapi-mesa 22.3.6-1+deb12u1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libglvnd0:amd64 libglvnd0 1.6.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 22.3.6-1+deb12u1 install ok installed libglx0:amd64 libglx0 1.6.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgprofng0:amd64 libgprofng0 2.40-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.33-2+deb12u1 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-2+deb12u1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.8+repack1-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-3 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-4 install ok installed libhtsjdk-java libhtsjdk-java 3.0.4+dfsg-2 install ok installed libhwloc15:amd64 libhwloc15 2.9.0-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libisal2 libisal2 2.30.0-5 install ok installed libisl23:amd64 libisl23 0.25-1.1 install ok installed libitm1:amd64 libitm1 12.2.0-14 install ok installed libjansson4:amd64 libjansson4 2.14-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjbzip2-java libjbzip2-java 0.9.1-8 install ok installed libjemalloc2:amd64 libjemalloc2 5.3.0-1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 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+dfsg1-3 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 2.6.2+ds1-5 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 5.3.0-4 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libjson-perl libjson-perl 4.10000-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed libllvm15:amd64 libllvm15 1:15.0.6-4+b1 install ok installed liblsan0:amd64 liblsan0 12.2.0-14 install ok installed liblua5.3-0:amd64 liblua5.3-0 5.3.6-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmjson-java libmjson-java 1.4.0-3 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libmpc3:amd64 libmpc3 1.3.1-1 install ok installed libmpfr6:amd64 libmpfr6 4.2.0-1 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.3+dfsg-6~deb12u1 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2 install ok installed libncurses6:amd64 libncurses6 6.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libngs-java:amd64 libngs-java 3.0.3+dfsg-6~deb12u1 install ok installed libngs-jni:amd64 libngs-jni 3.0.3+dfsg-6~deb12u1 install ok installed libnlopt0:amd64 libnlopt0 2.7.1-5 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.35-1 install ok installed libnss3:amd64 libnss3 2:3.87.1-1 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.21+ds-4 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.21+ds-4 install ok installed libopenblas0:amd64 libopenblas0 0.3.21+ds-4 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.21+ds-4 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpcsclite1:amd64 libpcsclite1 1.9.9-2 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.2-1+b1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.2-1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11:amd64 libpython3.11 3.11.2-6+deb12u2 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.2-6+deb12u2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-5 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libraqm0:amd64 libraqm0 0.7.0-4.1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librhino-java librhino-java 1.7.14-2.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsensors-config libsensors-config 1:3.6.0-7.1 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-7.1 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsis-base-java libsis-base-java 18.09~pre1+git20180928.45fbd31+dfsg-3 install ok installed libsis-base-jni libsis-base-jni 18.09~pre1+git20180928.45fbd31+dfsg-3 install ok installed libsis-jhdf5-java libsis-jhdf5-java 19.04.1+dfsg-3 install ok installed libsis-jhdf5-jni libsis-jhdf5-jni 19.04.1+dfsg-3 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libsnappy-java libsnappy-java 1.1.8.3-1 install ok installed libsnappy-jni libsnappy-jni 1.1.8.3-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.9-3 install ok installed libsodium23:amd64 libsodium23 1.0.18-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstaden-read14:amd64 libstaden-read14 1.14.15-1 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.2.0-14 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libsz2:amd64 libsz2 1.0.6-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtbb12:amd64 libtbb12 2021.8.0-2 install ok installed libtbbbind-2-5:amd64 libtbbbind-2-5 2021.8.0-2 install ok installed libtbbmalloc2:amd64 libtbbmalloc2 2021.8.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 12.2.0-14 install ok installed libubsan1:amd64 libubsan1 12.2.0-14 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libuv1:amd64 libuv1 1.44.2-1+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2+deb12u1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.15-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.15-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.15-1 install ok installed libxcb-present0:amd64 libxcb-present0 1.15-1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.15-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.15-1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.1-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxi6:amd64 libxi6 2:1.8-1+b1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.2-2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxsimd-dev:amd64 libxsimd-dev 8.1.0-7 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.1.99-1 install ok installed littler littler 0.3.17-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed megadepth megadepth 1.2.0-4 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed multiqc multiqc 1.14+dfsg-1 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed node-bootstrap-sass node-bootstrap-sass 3.4.3-2 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.12+7-2~deb12u1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.12+7-2~deb12u1 install ok installed openssl openssl 3.0.13-1~deb12u2 install ok installed pandoc pandoc 2.17.1.1-2~deb12u1 install ok installed pandoc-data pandoc-data 2.17.1.1-2~deb12u1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed pigx-rnaseq pigx-rnaseq 0.1.0-1.1 install ok installed pigz pigz 2.6-1 install ok installed python-babel-localedata python-babel-localedata 2.10.3-1 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-adal python3-adal 1.2.7-2 install ok installed python3-aiohttp python3-aiohttp 3.8.4-1 install ok installed python3-aiosignal python3-aiosignal 1.3.1-1 install ok installed python3-alabaster python3-alabaster 0.7.12-1 install ok installed python3-all python3-all 3.11.2-1+b1 install ok installed python3-all-dev python3-all-dev 3.11.2-1+b1 install ok installed python3-appdirs python3-appdirs 1.4.4-3 install ok installed python3-async-timeout python3-async-timeout 4.0.2-1 install ok installed python3-attr python3-attr 22.2.0-1 install ok installed python3-avro python3-avro 1.11.1+dfsg-2 install ok installed python3-azure python3-azure 20230112+git-1 install ok installed python3-azure-storage python3-azure-storage 20230112+git-1 install ok installed python3-babel python3-babel 2.10.3-1 install ok installed python3-bcrypt python3-bcrypt 3.2.2-1 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-blinker python3-blinker 1.5-1 install ok installed python3-boto3 python3-boto3 1.26.27+dfsg-1 install ok installed python3-botocore python3-botocore 1.29.27+repack-1 install ok installed python3-brotli python3-brotli 1.0.9-2+b6 install ok installed python3-certifi python3-certifi 2022.9.24-1 install ok installed python3-cffi-backend:amd64 python3-cffi-backend 1.15.1-5+b1 install ok installed python3-chardet python3-chardet 5.1.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.0.1-2 install ok installed python3-click python3-click 8.1.3-2 install ok installed python3-colorama python3-colorama 0.4.6-2 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 1.5.3-1 install ok installed python3-connection-pool python3-connection-pool 0.0.3-2 install ok installed python3-contourpy python3-contourpy 1.0.7-1+b1 install ok installed python3-cryptography python3-cryptography 38.0.4-3 install ok installed python3-cutadapt python3-cutadapt 4.2-1+b1 install ok installed python3-cycler python3-cycler 0.11.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-2 install ok installed python3-datrie:amd64 python3-datrie 0.8.2-4+b1 install ok installed python3-decorator python3-decorator 5.1.1-3 install ok installed python3-deeptools python3-deeptools 3.5.1-3 install ok installed python3-deeptoolsintervals python3-deeptoolsintervals 0.1.9-3+b6 install ok installed python3-dev python3-dev 3.11.2-1+b1 install ok installed python3-distutils python3-distutils 3.11.2-3 install ok installed python3-dnaio python3-dnaio 0.10.0-1+b1 install ok installed python3-docutils python3-docutils 0.19+dfsg-6 install ok installed python3-fastjsonschema python3-fastjsonschema 2.16.3-2 install ok installed python3-fonttools python3-fonttools 4.38.0-1+b1 install ok installed python3-frozenlist python3-frozenlist 1.3.3-1+b1 install ok installed python3-fs python3-fs 2.4.16-2 install ok installed python3-future python3-future 0.18.2-6 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-gi python3-gi 3.42.2-3+b1 install ok installed python3-git python3-git 3.1.30-1+deb12u2 install ok installed python3-gitdb python3-gitdb 4.0.9-2 install ok installed python3-htseq python3-htseq 1.99.2-1+b3 install ok installed python3-humanfriendly python3-humanfriendly 10.0-3 install ok installed python3-idna python3-idna 3.3-1+deb12u1 install ok installed python3-imagesize python3-imagesize 1.4.1-1 install ok installed python3-isodate python3-isodate 0.6.1-1 install ok installed python3-jinja2 python3-jinja2 3.1.2-1 install ok installed python3-jmespath python3-jmespath 1.0.1-1 install ok installed python3-jsonschema python3-jsonschema 4.10.3-1 install ok installed python3-jupyter-core python3-jupyter-core 4.12.0-1 install ok installed python3-jwt python3-jwt 2.6.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-1+b1 install ok installed python3-lib2to3 python3-lib2to3 3.11.2-3 install ok installed python3-lxml:amd64 python3-lxml 4.9.2-1+b1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b2 install ok installed python3-lzstring python3-lzstring 1.0.4-2 install ok installed python3-markdown python3-markdown 3.4.1-2 install ok installed python3-markdown-it python3-markdown-it 2.1.0-5 install ok installed python3-markupsafe python3-markupsafe 2.1.2-1+b1 install ok installed python3-marshmallow python3-marshmallow 3.18.0-1 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b1 install ok installed python3-mdurl python3-mdurl 0.1.2-1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-mpmath python3-mpmath 1.2.1-2 install ok installed python3-msal python3-msal 1.21.0-1 install ok installed python3-msal-extensions python3-msal-extensions 1.0.0-2 install ok installed python3-msrest python3-msrest 0.6.21-2 install ok installed python3-msrestazure python3-msrestazure 0.6.4-2 install ok installed python3-multidict python3-multidict 6.0.4-1+b1 install ok installed python3-nacl python3-nacl 1.5.0-2 install ok installed python3-nbformat python3-nbformat 5.5.0-1 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-numpydoc python3-numpydoc 1.5.0-1 install ok installed python3-oauthlib python3-oauthlib 3.2.2-1 install ok installed python3-packaging python3-packaging 23.0-1 install ok installed python3-paramiko python3-paramiko 2.12.0-2 install ok installed python3-pbr python3-pbr 5.10.0-2 install ok installed python3-pil:amd64 python3-pil 9.4.0-1.1+deb12u1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 9.4.0-1.1+deb12u1 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-plotly python3-plotly 5.4.1+dfsg-1 install ok installed python3-ply python3-ply 3.11-5 install ok installed python3-portalocker python3-portalocker 2.2.1-1 install ok installed python3-psutil python3-psutil 5.9.4-1+b1 install ok installed python3-pulp python3-pulp 2.6.0+dfsg-1 install ok installed python3-py python3-py 1.11.0-1 install ok installed python3-py2bit python3-py2bit 0.3.1-1+b2 install ok installed python3-pybigwig python3-pybigwig 0.3.18+dfsg-1+b3 install ok installed python3-pygments python3-pygments 2.14.0+dfsg-1 install ok installed python3-pyparsing python3-pyparsing 3.0.9-1 install ok installed python3-pyrsistent:amd64 python3-pyrsistent 0.18.1-1+b3 install ok installed python3-pysam python3-pysam 0.20.0+ds-3+b1 install ok installed python3-pythran python3-pythran 0.11.0+ds-7 install ok installed python3-ratelimiter python3-ratelimiter 1.2.0.post0-4 install ok installed python3-requests python3-requests 2.28.1+dfsg-1 install ok installed python3-requests-oauthlib python3-requests-oauthlib 1.3.0+ds-1 install ok installed python3-retry python3-retry 0.9.2-2 install ok installed python3-rich python3-rich 13.3.1-1 install ok installed python3-rich-click python3-rich-click 1.6.0-1 install ok installed python3-roman python3-roman 3.3-3 install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.17.21-1 install ok installed python3-ruamel.yaml.clib:amd64 python3-ruamel.yaml.clib 0.2.7-1+b2 install ok installed python3-s3transfer python3-s3transfer 0.6.0-1 install ok installed python3-scipy python3-scipy 1.10.1-2 install ok installed python3-setuptools python3-setuptools 66.1.1-1 install ok installed python3-simplejson python3-simplejson 3.18.3-1 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-smart-open python3-smart-open 5.2.1-5 install ok installed python3-smmap python3-smmap 5.0.0-1 install ok installed python3-snowballstemmer python3-snowballstemmer 2.2.0-2 install ok installed python3-spectra python3-spectra 0.0.11-4 install ok installed python3-sphinx python3-sphinx 5.3.0-4 install ok installed python3-stopit python3-stopit 1.1.2-2 install ok installed python3-strictyaml python3-strictyaml 1.6.1-3 install ok installed python3-sympy python3-sympy 1.11.1-1 install ok installed python3-tabulate python3-tabulate 0.8.9-1 install ok installed python3-tenacity python3-tenacity 8.2.1-1 install ok installed python3-throttler python3-throttler 1.2.2-2 install ok installed python3-tk:amd64 python3-tk 3.11.2-3 install ok installed python3-toposort python3-toposort 1.9-1 install ok installed python3-tqdm python3-tqdm 4.64.1-1 install ok installed python3-traitlets python3-traitlets 5.5.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.4.0-1 install ok installed python3-tz python3-tz 2022.7.1-4 install ok installed python3-uamqp python3-uamqp 1.5.3-1+b4 install ok installed python3-ufolib2 python3-ufolib2 0.14.0+dfsg1-1 install ok installed python3-urllib3 python3-urllib3 1.26.12-1 install ok installed python3-wrapt python3-wrapt 1.14.1-2+b2 install ok installed python3-xopen python3-xopen 1.7.0-2 install ok installed python3-yaml python3-yaml 6.0-3+b2 install ok installed python3-yarl python3-yarl 1.8.2-1+b1 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-dev python3.11-dev 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed r-base-core r-base-core 4.2.2.20221110-2 install ok installed r-bioc-annotate r-bioc-annotate 1.76.0+dfsg-1 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.60.0-1 install ok installed r-bioc-biobase r-bioc-biobase 2.58.0-2 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.44.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.8.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.32.5-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.66.0-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.24.0+dfsg-1 install ok installed r-bioc-deseq2 r-bioc-deseq2 1.38.3+dfsg-1 install ok installed r-bioc-geneplotter r-bioc-geneplotter 1.76.0-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.34.9-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.9-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.34.0-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.50.2+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.32.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.38.0+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.10.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.14.0-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.58.0-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.36.1-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.28.0+dfsg-1 install ok installed r-bioc-tximport r-bioc-tximport 1.26.1+dfsg-1 install ok installed r-bioc-xvector r-bioc-xvector 0.38.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.44.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 install ok installed r-cran-askpass r-cran-askpass 1.1-2 install ok installed r-cran-backports r-cran-backports 1.4.1-1 install ok installed r-cran-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.74.0-2 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.3-1 install ok installed r-cran-boot r-cran-boot 1.3-28.1-1 install ok installed r-cran-brio r-cran-brio 1.1.3-1+b1 install ok installed r-cran-broom r-cran-broom 1.0.3+dfsg-2 install ok installed r-cran-bslib r-cran-bslib 0.4.2+dfsg-1 install ok installed r-cran-cachem r-cran-cachem 1.0.7-1 install ok installed r-cran-callr r-cran-callr 3.7.3-2 install ok installed r-cran-car r-cran-car 3.1-1-1 install ok installed r-cran-cardata r-cran-cardata 3.0.5-1 install ok installed r-cran-caret r-cran-caret 6.0-93+dfsg-1 install ok installed r-cran-cellranger r-cran-cellranger 1.1.0-3 install ok installed r-cran-class r-cran-class 7.3-21-1 install ok installed r-cran-cli r-cran-cli 3.6.0-1 install ok installed r-cran-clipr r-cran-clipr 0.8.0-1 install ok installed r-cran-clock r-cran-clock 0.6.1-2 install ok installed r-cran-codetools r-cran-codetools 0.2-19-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-colourpicker r-cran-colourpicker 1.2.0+dfsg-1 install ok installed r-cran-commonmark r-cran-commonmark 1.8.1-1 install ok installed r-cran-conquer r-cran-conquer 1.3.2-1 install ok installed r-cran-corrplot r-cran-corrplot 0.92-1 install ok installed r-cran-cowplot r-cran-cowplot 1.1.1+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.4.3-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-crosstalk r-cran-crosstalk 1.2.0+dfsg-1 install ok installed r-cran-curl r-cran-curl 5.0.0+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.14.8+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.1.3-1 install ok installed r-cran-desc r-cran-desc 1.4.2-1 install ok installed r-cran-diffobj r-cran-diffobj 0.3.5-1+b1 install ok installed r-cran-digest r-cran-digest 0.6.31-1 install ok installed r-cran-dplyr r-cran-dplyr 1.0.10-1 install ok installed r-cran-dt r-cran-dt 0.27+dfsg-1 install ok installed r-cran-e1071 r-cran-e1071 1.7-13-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 0.20-1 install ok installed r-cran-fansi r-cran-fansi 1.0.4-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-fontawesome r-cran-fontawesome 0.5.0-1 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 0.8.84-1 install ok installed r-cran-formatr r-cran-formatr 1.14-1 install ok installed r-cran-fs r-cran-fs 1.6.1+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 1.31.0+dfsg-1 install ok installed r-cran-future.apply r-cran-future.apply 1.10.0+dfsg-1 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.1+dfsg-1 install ok installed r-cran-ggpubr r-cran-ggpubr 0.6.0-1 install ok installed r-cran-ggrepel r-cran-ggrepel 0.9.3-1 install ok installed r-cran-ggsci r-cran-ggsci 2.9-3 install ok installed r-cran-ggsignif r-cran-ggsignif 0.6.4-1 install ok installed r-cran-globals r-cran-globals 0.16.2-1 install ok installed r-cran-glue r-cran-glue 1.6.2-1 install ok installed r-cran-gower r-cran-gower 1.0.1-1 install ok installed r-cran-gprofiler2 r-cran-gprofiler2 0.2.1+dfsg-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.1+dfsg-1 install ok installed r-cran-hardhat r-cran-hardhat 1.2.0+dfsg-1 install ok installed r-cran-haven r-cran-haven 2.5.1-1 install ok installed r-cran-highr r-cran-highr 0.10+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.2-1 install ok installed r-cran-htmltools r-cran-htmltools 0.5.4-1 install ok installed r-cran-htmlwidgets r-cran-htmlwidgets 1.6.1+dfsg-1 install ok installed r-cran-httpuv r-cran-httpuv 1.6.9+dfsg-1 install ok installed r-cran-httr r-cran-httr 1.4.5+dfsg-1 install ok installed r-cran-ipred r-cran-ipred 0.9-13-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-jquerylib r-cran-jquerylib 0.1.4+dfsg-4 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.4+dfsg-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-20-1 install ok installed r-cran-knitr r-cran-knitr 1.42+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-later r-cran-later 1.3.0+dfsg-1+b1 install ok installed r-cran-lattice r-cran-lattice 0.20-45-3 install ok installed r-cran-lava r-cran-lava 1.7.2.1+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 1.0.3+dfsg-1 install ok installed r-cran-listenv r-cran-listenv 0.9.0+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.17-1 install ok installed r-cran-lme4 r-cran-lme4 1.1-31-1 install ok installed r-cran-locfit r-cran-locfit 1.5-9.7-1 install ok installed r-cran-lubridate r-cran-lubridate 1.9.2+dfsg-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-maptools r-cran-maptools 1:1.1-6+dfsg-1 install ok installed r-cran-mass r-cran-mass 7.3-58.2-1 install ok installed r-cran-matrix r-cran-matrix 1.5-3-1 install ok installed r-cran-matrixmodels r-cran-matrixmodels 0.5-1-1 install ok installed r-cran-matrixstats r-cran-matrixstats 0.63.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-41-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-miniui r-cran-miniui 0.1.1.1-3 install ok installed r-cran-minqa r-cran-minqa 1.2.5-1 install ok installed r-cran-modelmetrics r-cran-modelmetrics 1.2.2.2-1+b1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.162-1 install ok installed r-cran-nloptr r-cran-nloptr 2.0.3-1 install ok installed r-cran-nnet r-cran-nnet 7.3-18-1 install ok installed r-cran-numderiv r-cran-numderiv 2016.8-1.1-3 install ok installed r-cran-openssl r-cran-openssl 2.0.5+dfsg-1 install ok installed r-cran-openxlsx r-cran-openxlsx 4.2.5.2-1 install ok installed r-cran-parallelly r-cran-parallelly 1.34.0-1 install ok installed r-cran-pbkrtest r-cran-pbkrtest 0.5.2-2 install ok installed r-cran-pheatmap r-cran-pheatmap 1.0.12-2 install ok installed r-cran-pillar r-cran-pillar 1.8.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.2-2 install ok installed r-cran-pkgload r-cran-pkgload 1.3.2-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-plotly r-cran-plotly 4.10.1+dfsg-2 install ok installed r-cran-plyr r-cran-plyr 1.8.8-1 install ok installed r-cran-png r-cran-png 0.1-8-1 install ok installed r-cran-polynom r-cran-polynom 1.4-1+dfsg-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-proc r-cran-proc 1.18.0-1+b1 install ok installed r-cran-processx r-cran-processx 3.8.0-1 install ok installed r-cran-prodlim r-cran-prodlim 2019.11.13-1+b1 install ok installed r-cran-progress r-cran-progress 1.2.2-2 install ok installed r-cran-progressr r-cran-progressr 0.13.0-1 install ok installed r-cran-promises r-cran-promises 1.2.0.1+dfsg-1 install ok installed r-cran-proxy r-cran-proxy 0.4-27-1 install ok installed r-cran-ps r-cran-ps 1.7.2-1 install ok installed r-cran-purrr r-cran-purrr 1.0.1-1 install ok installed r-cran-quantreg r-cran-quantreg 5.94-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.10-1 install ok installed r-cran-rcpparmadillo r-cran-rcpparmadillo 0.12.0.1.0-1 install ok installed r-cran-rcppeigen r-cran-rcppeigen 0.3.3.9.3-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.10+dfsg-1 install ok installed r-cran-readr r-cran-readr 2.1.4-1 install ok installed r-cran-readxl r-cran-readxl 1.4.2-1 install ok installed r-cran-recipes r-cran-recipes 1.0.4+dfsg-1 install ok installed r-cran-rematch r-cran-rematch 1.0.1-3 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 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 0.5.29-1 install ok installed r-cran-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.0.6-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.20+dfsg-1 install ok installed r-cran-rpart r-cran-rpart 4.1.19-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.3-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.2.20-1 install ok installed r-cran-rstatix r-cran-rstatix 0.7.2-1 install ok installed r-cran-sass r-cran-sass 0.4.5+dfsg-1 install ok installed r-cran-scales r-cran-scales 1.2.1-1 install ok installed r-cran-shiny r-cran-shiny 1.7.4+dfsg-2+deb12u1 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-sp r-cran-sp 1:1.6-0+dfsg-1 install ok installed r-cran-sparsem r-cran-sparsem 1.81-1 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 1.7.12-1 install ok installed r-cran-stringr r-cran-stringr 1.5.0-1 install ok installed r-cran-survival r-cran-survival 3.5-3-1 install ok installed r-cran-sys r-cran-sys 3.4.1-1 install ok installed r-cran-testthat r-cran-testthat 3.1.6-1 install ok installed r-cran-tibble r-cran-tibble 3.1.8+dfsg-1 install ok installed r-cran-tidyr r-cran-tidyr 1.3.0-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-timechange r-cran-timechange 0.2.0-1 install ok installed r-cran-timedate r-cran-timedate 4022.108-1 install ok installed r-cran-tinytex r-cran-tinytex 0.44-1 install ok installed r-cran-tzdb r-cran-tzdb 0.3.0-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.5.2-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.1-1 install ok installed r-cran-vroom r-cran-vroom 1.6.1-1 install ok installed r-cran-waldo r-cran-waldo 0.4.0-1 install ok installed r-cran-withr r-cran-withr 2.5.0-1 install ok installed r-cran-xfun r-cran-xfun 0.37+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.13-1 install ok installed r-cran-xtable r-cran-xtable 1:1.8-4-2 install ok installed r-cran-yaml r-cran-yaml 2.3.7-1 install ok installed r-cran-zip r-cran-zip 2.2.2-1+b1 install ok installed readline-common readline-common 8.2-1.3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed salmon salmon 1.10.1+ds1-1+b1 install ok installed samtools samtools 1.16.1-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed sgml-base sgml-base 1.31 install ok installed shared-mime-info shared-mime-info 2.2-1 install ok installed snakemake snakemake 7.21.0-1 install ok installed sphinx-common sphinx-common 5.3.0-4 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-4.1 install ok installed trim-galore trim-galore 0.6.10-1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unicode-data unicode-data 15.0.0-1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.13.dfsg-1 6m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 6m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'remove', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cpp', 'cpp-12', 'cutadapt', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'gir1.2-glib-2.0:amd64', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libaec0:amd64', 'libapache-pom-java', 'libargs4j-java', 'libasan8:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgirepository-1.0-1:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnlopt0:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libopenblas-dev:amd64', 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'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-tqdm', 'python3-traitlets', 'python3-typing-extensions', 'python3-tz', 'python3-uamqp', 'python3-ufolib2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yarl', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', '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-blob', 'r-cran-boot', 'r-cran-brio', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-callr', '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-dbi', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', '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-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-maptools', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', '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-pkgload', 'r-cran-plogr', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-png', 'r-cran-polynom', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-processx', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-ps', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sp', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-testthat', '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-waldo', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 6m57.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adwaita-icon-theme at-spi2-common binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates ca-certificates-java coinor-cbc coinor-libcbc3 coinor-libcgl1 coinor-libclp1 coinor-libcoinutils3v5 coinor-libosi1v5 cpp cpp-12 cutadapt default-jre default-jre-headless docutils-common fastp fastqc fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-glyphicons-halflings fonts-lyx fonts-mathjax g++ g++-12 gcc gcc-12 gir1.2-glib-2.0 git git-man gtk-update-icon-cache hicolor-icon-theme hisat2 java-common javascript-common libaec0 libapache-pom-java libargs4j-java libasan8 libasound2 libasound2-data libatk1.0-0 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbigwig0 libbinutils libblas3 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcommons-compress-java libcommons-io-java 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littler media-types megadepth multiqc ncbi-vdb-data node-bootstrap-sass node-html5shiv node-normalize.css openjdk-17-jre openjdk-17-jre-headless openssl pandoc pandoc-data perl perl-modules-5.36 pigx-rnaseq pigz python-babel-localedata python-matplotlib-data python3 python3-adal python3-aiohttp python3-aiosignal python3-alabaster python3-all python3-all-dev python3-appdirs python3-async-timeout python3-attr python3-avro python3-azure python3-azure-storage python3-babel python3-bcrypt python3-beniget python3-blinker python3-boto3 python3-botocore python3-brotli python3-certifi python3-cffi-backend python3-chardet python3-charset-normalizer python3-click python3-colorama python3-coloredlogs python3-colormath python3-configargparse python3-connection-pool python3-contourpy python3-cryptography python3-cutadapt python3-cycler python3-dateutil python3-datrie python3-decorator python3-deeptools python3-deeptoolsintervals python3-dev python3-distutils python3-dnaio python3-docutils python3-fastjsonschema python3-fonttools python3-frozenlist python3-fs python3-future python3-gast python3-gi python3-git python3-gitdb python3-htseq python3-humanfriendly python3-idna python3-imagesize python3-isodate python3-jinja2 python3-jmespath python3-jsonschema python3-jupyter-core python3-jwt python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-lzstring python3-markdown python3-markdown-it python3-markupsafe python3-marshmallow python3-matplotlib python3-mdurl python3-minimal python3-mpmath python3-msal python3-msal-extensions python3-msrest python3-msrestazure python3-multidict python3-nacl python3-nbformat python3-networkx python3-numpy python3-numpydoc python3-oauthlib python3-packaging python3-paramiko python3-pbr python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-ply python3-portalocker python3-psutil python3-pulp python3-py python3-py2bit python3-pybigwig python3-pygments python3-pyparsing python3-pyrsistent python3-pysam python3-pythran python3-ratelimiter python3-requests python3-requests-oauthlib python3-retry python3-rich python3-rich-click python3-roman python3-ruamel.yaml python3-ruamel.yaml.clib python3-s3transfer python3-scipy python3-setuptools python3-simplejson python3-six python3-smart-open python3-smmap python3-snowballstemmer python3-spectra python3-sphinx python3-stopit python3-strictyaml python3-sympy python3-tabulate python3-tenacity python3-throttler python3-tk python3-toposort python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-uamqp python3-ufolib2 python3-urllib3 python3-wrapt python3-xopen python3-yaml python3-yarl python3.11 python3.11-dev python3.11-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport 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-blob r-cran-boot r-cran-brio r-cran-broom r-cran-bslib r-cran-cachem r-cran-callr 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-dbi r-cran-desc r-cran-diffobj r-cran-digest 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-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-maptools r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-miniui r-cran-minqa r-cran-modelmetrics 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-pkgload r-cran-plogr r-cran-plotly r-cran-plyr r-cran-png r-cran-polynom r-cran-praise r-cran-prettyunits r-cran-proc r-cran-processx r-cran-prodlim r-cran-progress r-cran-progressr r-cran-promises r-cran-proxy r-cran-ps r-cran-purrr r-cran-quantreg r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rcurl r-cran-readr r-cran-readxl r-cran-recipes r-cran-rematch r-cran-rematch2 r-cran-reshape2 r-cran-restfulr r-cran-rio r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rpart r-cran-rprojroot r-cran-rsqlite r-cran-rstatix r-cran-sass r-cran-scales r-cran-shiny r-cran-shinyjs r-cran-snow r-cran-sourcetools r-cran-sp r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat 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-waldo r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml r-cran-zip readline-common rpcsvc-proto salmon samtools sensible-utils sgml-base shared-mime-info snakemake sphinx-common tk8.6-blt2.5 trim-galore ucf unicode-data unzip x11-common xdg-utils xml-core zip zlib1g-dev 0 upgraded, 0 newly installed, 693 to remove and 0 not upgraded. After this operation, 2946 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 ... 126816 files and directories currently installed.) Removing pigx-rnaseq (0.1.0-1.1) ... Removing fastqc (0.11.9+dfsg-6) ... Removing default-jre (2:1.17-74) ... Removing openjdk-17-jre:amd64 (17.0.12+7-2~deb12u1) ... Removing libgtk2.0-0:amd64 (2.24.33-2+deb12u1) ... Removing adwaita-icon-theme (43-1) ... Removing libatk1.0-0:amd64 (2.46.0-5) ... Removing at-spi2-common (2.46.0-5) ... Removing python3-deeptools (3.5.1-3) ... Removing g++ (4:12.2.0-3) ... Removing gcc (4:12.2.0-3) ... Removing multiqc (1.14+dfsg-1) ... Removing python3-matplotlib (3.6.3-1+b1) ... Removing default-jre-headless (2:1.17-74) ... Removing snakemake (7.21.0-1) ... Removing python3-pulp (2.6.0+dfsg-1) ... Removing coinor-cbc (2.10.8+ds1-1) ... Removing coinor-libcbc3:amd64 (2.10.8+ds1-1) ... Removing coinor-libcgl1:amd64 (0.60.3+repack1-4) ... Removing coinor-libclp1:amd64 (1.17.6-3) ... Removing coinor-libosi1v5:amd64 (0.108.6+repack1-2) ... Removing coinor-libcoinutils3v5:amd64 (2.11.4+repack1-2) ... Removing cpp (4:12.2.0-3) ... Removing trim-galore (0.6.10-1) ... Removing cutadapt (4.2-1) ... Removing python3-numpydoc (1.5.0-1) ... Removing python3-sphinx (5.3.0-4) ... Removing python3-docutils (0.19+dfsg-6) ... Removing docutils-common (0.19+dfsg-6) ... Removing fastp (0.23.2+dfsg-2+b1) ... Removing r-cran-ggpubr (0.6.0-1) ... Removing r-cran-rstatix (0.7.2-1) ... Removing r-cran-car (3.1-1-1) ... Removing r-cran-quantreg (5.94-1) ... Removing r-cran-conquer (1.3.2-1) ... Removing r-cran-caret (6.0-93+dfsg-1) ... Removing r-cran-recipes (1.0.4+dfsg-1) ... Removing r-cran-ipred (0.9-13-1) ... Removing r-cran-rpart (4.1.19-1) ... Removing r-cran-prodlim (2019.11.13-1+b1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-bioc-rtracklayer (1.58.0-1) ... Removing r-cran-pbkrtest (0.5.2-2) ... Removing r-cran-lme4 (1.1-31-1) ... Removing r-cran-rcppeigen (0.3.3.9.3-1) ... Removing python-matplotlib-data (3.6.3-1) ... Removing r-cran-gprofiler2 (0.2.1+dfsg-1) ... Removing r-cran-plotly (4.10.1+dfsg-2) ... Removing r-cran-colourpicker (1.2.0+dfsg-1) ... Removing r-cran-shinyjs (2.1.0-1) ... Removing r-cran-dt (0.27+dfsg-1) ... Removing r-cran-htmlwidgets (1.6.1+dfsg-1) ... Removing r-cran-rmarkdown (2.20+dfsg-1) ... Removing r-cran-knitr (1.42+dfsg-1) ... Removing r-cran-crosstalk (1.2.0+dfsg-1) ... Removing fonts-lyx (2.3.7-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing python3-smart-open (5.2.1-5) ... Removing python3-git (3.1.30-1+deb12u2) ... Removing git (1:2.39.2-1.1) ... Removing git-man (1:2.39.2-1.1) ... Removing gtk-update-icon-cache (3.24.38-2~deb12u2) ... Removing hicolor-icon-theme (0.17-2) ... Removing hisat2 (2.2.1-4+b2) ... Removing libsis-jhdf5-java (19.04.1+dfsg-3) ... Removing libsis-jhdf5-jni (19.04.1+dfsg-3) ... Removing libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Removing libsz2:amd64 (1.0.6-1+b1) ... Removing libaec0:amd64 (1.0.6-1+b1) ... Removing libhtsjdk-java (3.0.4+dfsg-2) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing libcommons-logging-java (1.2-3) ... Removing libcommons-lang3-java (3.12.0-2) ... Removing libargs4j-java (2.33-2) ... Removing megadepth (1.2.0-4) ... Removing python3-pybigwig (0.3.18+dfsg-1+b3) ... Removing libbigwig0:amd64 (0.4.7+dfsg-3) ... 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Removing python3-roman (3.3-3) ... Removing python3-simplejson (3.18.3-1) ... Removing python3-wrapt (1.14.1-2+b2) ... Removing python3-smmap (5.0.0-1) ... Removing python3-snowballstemmer (2.2.0-2) ... Removing python3-tabulate (0.8.9-1) ... Removing python3-throttler (1.2.2-2) ... Removing python3-toposort (1.9-1) ... Removing r-bioc-biobase (2.58.0-2) ... Removing r-bioc-delayedarray (0.24.0+dfsg-1) ... Removing r-bioc-biocio (1.8.0+dfsg-1) ... Removing r-bioc-tximport (1.26.1+dfsg-1) ... Removing r-bioc-matrixgenerics (1.10.0-1) ... Removing r-cran-backports (1.4.1-1) ... Removing r-cran-miniui (0.1.1.1-3) ... Removing r-cran-vroom (1.6.1-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.3-1) ... Removing r-cran-boot (1.3-28.1-1) ... Removing r-cran-testthat (3.1.6-1) ... Removing r-cran-brio (1.1.3-1+b1) ... Removing r-cran-callr (3.7.3-2) ... Removing r-cran-cardata (3.0.5-1) ... Removing r-cran-readxl (1.4.2-1) ... Removing r-cran-cellranger (1.1.0-3) ... Removing r-cran-e1071 (1.7-13-1) ... Removing r-cran-class (7.3-21-1) ... Removing r-cran-waldo (0.4.0-1) ... Removing r-cran-progress (1.2.2-2) ... Removing r-cran-hms (1.1.2-1) ... Removing r-cran-clipr (0.8.0-1) ... Removing r-cran-clock (0.6.1-2) ... Removing r-cran-lava (1.7.2.1+dfsg-1) ... Removing r-cran-future.apply (1.10.0+dfsg-1) ... Removing r-cran-future (1.31.0+dfsg-1) ... Removing r-cran-globals (0.16.2-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-pheatmap (1.0.12-2) ... Removing r-cran-ggsci (2.9-3) ... Removing r-cran-corrplot (0.92-1) ... Removing r-cran-cowplot (1.1.1+dfsg-1) ... Removing r-cran-tzdb (0.3.0-1) ... Removing r-cran-lubridate (1.9.2+dfsg-1) ... Removing r-cran-timechange (0.2.0-1) ... Removing r-cran-pkgload (1.3.2-1) ... Removing r-cran-dbi (1.1.3-1) ... Removing r-cran-desc (1.4.2-1) ... Removing r-cran-diffobj (0.3.5-1+b1) ... Removing r-cran-progressr (0.13.0-1) ... Removing r-cran-dplyr (1.0.10-1) ... Removing r-cran-forcats (1.0.0-1) ... Removing r-cran-evaluate (0.20-1) ... Removing r-cran-hardhat (1.2.0+dfsg-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-maptools (1:1.1-6+dfsg-1) ... Removing r-cran-foreign (0.8.84-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-ggrepel (0.9.3-1) ... Removing r-cran-tidyselect (1.2.0+dfsg-1) ... Removing r-cran-purrr (1.0.1-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-kernsmooth (2.23-20-1) ... Removing r-cran-sp (1:1.6-0+dfsg-1) ... Removing r-cran-locfit (1.5-9.7-1) ... Removing r-cran-lazyeval (0.2.2-1+b1) ... Removing r-cran-listenv (0.9.0+dfsg-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-matrixmodels (0.5-1-1) ... Removing r-cran-matrixstats (0.63.0-1) ... Removing r-cran-minqa (1.2.5-1) ... Removing r-cran-nnet (7.3-18-1) ... Removing r-cran-numderiv (2016.8-1.1-3) ... Removing r-cran-parallelly (1.34.0-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-proc (1.18.0-1+b1) ... Removing r-cran-plyr (1.8.8-1) ... Removing r-cran-polynom (1.4-1+dfsg-1) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-processx (3.8.0-1) ... Removing r-cran-proxy (0.4-27-1) ... Removing r-cran-ps (1.7.2-1) ... Removing r-cran-rematch (1.0.1-3) ... Removing r-cran-rprojroot (2.0.3-1) ... Removing r-cran-sparsem (1.81-1) ... Removing r-cran-squarem (2021.1-1) ... Removing r-cran-statmod (1.5.0-1) ... Removing r-cran-timedate (4022.108-1) ... Removing r-cran-tinytex (0.44-1) ... Removing r-cran-xfun (0.37+dfsg-1) ... Removing r-cran-yaml (2.3.7-1) ... Removing r-cran-zip (2.2.2-1+b1) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... Removing openjdk-17-jre-headless:amd64 (17.0.12+7-2~deb12u1) ... Removing ca-certificates-java (20230710~deb12u1) ... Removing r-cran-survival (3.5-3-1) ... Removing r-bioc-rsamtools (2.14.0-1) ... Removing r-bioc-biocparallel (1.32.5-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-shiny (1.7.4+dfsg-2+deb12u1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing java-common (0.74) ... Removing r-cran-bslib (0.4.2+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (11+nmu1) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing r-cran-bh (1.74.0-2) ... Removing libasound2:amd64 (1.2.8-1+b1) ... Removing libasound2-data (1.2.8-1) ... Removing libcups2:amd64 (2.4.2-3+deb12u7) ... Removing libavahi-client3:amd64 (0.8-10) ... Removing libavahi-common3:amd64 (0.8-10) ... Removing libavahi-common-data:amd64 (0.8-10) ... Removing r-cran-ggplot2 (3.4.1+dfsg-1) ... Removing r-cran-mgcv (1.8-41-1) ... Removing r-cran-httr (1.4.5+dfsg-1) ... Removing r-cran-curl (5.0.0+dfsg-1) ... Removing r-bioc-genomicranges (1.50.2+dfsg-1) ... Removing r-bioc-biostrings (2.66.0-1) ... Removing r-bioc-xvector (0.38.0-1) ... Removing r-bioc-rhtslib (2.0.0+dfsg-1) ... Removing r-bioc-zlibbioc (1.44.0+dfsg-1) ... Removing libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... Removing libhts3:amd64 (1.16+ds-3) ... Removing libdrm2:amd64 (2.4.114-1+b1) ... Removing libdrm-common (2.4.114-1) ... Removing python3-traitlets (5.5.0-1) ... Removing libhtscodecs2:amd64 (1.3.0-4) ... 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) ... 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Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-scales (1.2.1-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-commonmark (1.8.1-1) ... Removing r-cran-cpp11 (0.4.3-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-digest (0.6.31-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-tibble (3.1.8+dfsg-1) ... Removing r-cran-pillar (1.8.1+dfsg-1) ... Removing r-cran-fansi (1.0.4-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-1) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-gtable (0.3.1+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.4+dfsg-1) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-promises (1.2.0.1+dfsg-1) ... Removing r-cran-later (1.3.0+dfsg-1+b1) ... 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Removing python3-aiosignal (1.3.1-1) ... Removing python3-fs (2.4.16-2) ... Removing python3-appdirs (1.4.4-3) ... Removing python3-async-timeout (4.0.2-1) ... Removing python3-jsonschema (4.10.3-1) ... Removing python3-avro (1.11.1+dfsg-2) ... Removing python3-beniget (0.4.1-3) ... Removing python3-blinker (1.5-1) ... Removing python3-brotli (1.0.9-2+b6) ... Removing python3-msal (1.21.0-1) ... Removing python3-requests (2.28.1+dfsg-1) ... Removing python3-uamqp (1.5.3-1+b4) ... Removing python3-certifi (2022.9.24-1) ... Removing python3-chardet (5.1.0+dfsg-2) ... Removing python3-charset-normalizer (3.0.1-2) ... Removing python3-colorama (0.4.6-2) ... Removing python3-strictyaml (1.6.1-3) ... Removing python3-dateutil (2.8.2-2) ... Removing python3-decorator (5.1.1-3) ... Removing python3-frozenlist (1.3.3-1+b1) ... Removing python3-gast (0.5.2-2) ... Removing python3-idna (3.3-1+deb12u1) ... Removing python3-jwt (2.6.0-1) ... Removing python3-lib2to3 (3.11.2-3) ... Removing python3-lz4 (4.0.2+dfsg-1+b2) ... Removing python3-marshmallow (3.18.0-1) ... Removing python3-sympy (1.11.1-1) ... Removing python3-mpmath (1.2.1-2) ... Removing python3-multidict (6.0.4-1+b1) ... Removing python3-packaging (23.0-1) ... Removing python3-pkg-resources (66.1.1-1) ... Removing python3-ply (3.11-5) ... Removing python3-portalocker (2.2.1-1) ... Removing python3-pyrsistent:amd64 (0.18.1-1+b3) ... Removing python3-ruamel.yaml (0.17.21-1) ... Removing python3-ruamel.yaml.clib:amd64 (0.2.7-1+b2) ... Removing python3-urllib3 (1.26.12-1) ... Removing python3-tqdm (4.64.1-1) ... Removing python3-tz (2022.7.1-4) ... Removing unicode-data (15.0.0-1) ... Removing python3-ufolib2 (0.14.0+dfsg1-1) ... Removing gcc-12 (12.2.0-14) ... Removing binutils (2.40-2) ... Removing binutils-x86-64-linux-gnu (2.40-2) ... Removing libgprofng0:amd64 (2.40-2) ... Removing libctf0:amd64 (2.40-2) ... Removing libbinutils:amd64 (2.40-2) ... Removing binutils-common:amd64 (2.40-2) ... Removing python3-pil.imagetk:amd64 (9.4.0-1.1+deb12u1) ... Removing python3-tk:amd64 (3.11.2-3) ... Removing blt (2.5.3+dfsg-4.1) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp-12 (12.2.0-14) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing python3-azure-storage (20230112+git-1) ... Removing libgcc-12-dev:amd64 (12.2.0-14) ... Removing libasan8:amd64 (12.2.0-14) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing libpython3.11-dev:amd64 (3.11.2-6+deb12u2) ... Removing zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Removing libexpat1-dev:amd64 (2.5.0-1) ... Removing libc6-dev:amd64 (2.36-9+deb12u8) ... Removing libc-dev-bin (2.36-9+deb12u8) ... Removing libcc1-0:amd64 (12.2.0-14) ... Removing libcrypt-dev:amd64 (1:4.4.33-2) ... Removing libctf-nobfd0:amd64 (2.40-2) ... Removing python3-cryptography (38.0.4-3) ... Removing libpython3.11:amd64 (3.11.2-6+deb12u2) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.3+ds-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libicu72:amd64 (72.1-3) ... Removing libisl23:amd64 (0.25-1.1) ... Removing libitm1:amd64 (12.2.0-14) ... Removing libjansson4:amd64 (2.14-2) ... Removing liblsan0:amd64 (12.2.0-14) ... Removing libmpc3:amd64 (1.3.1-1) ... Removing libmpfr6:amd64 (4.2.0-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing openssl (3.0.13-1~deb12u2) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libtsan2:amd64 (12.2.0-14) ... Removing libubsan1:amd64 (12.2.0-14) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing linux-libc-dev:amd64 (6.1.99-1) ... Removing python3-attr (22.2.0-1) ... Removing python3-cffi-backend:amd64 (1.15.1-5+b1) ... Removing python3-isodate (0.6.1-1) ... Removing python3-six (1.16.0-4) ... Removing python3-typing-extensions (4.4.0-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4-4) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libtirpc-common (1.3.3+ds-1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 6m57.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'remove', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cpp', 'cpp-12', 'cutadapt', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'g++-', 'g++-12', 'gcc', 'gcc-12', 'gir1.2-glib-2.0:amd64', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libaec0:amd64', 'libapache-pom-java', 'libargs4j-java', 'libasan8:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgirepository-1.0-1:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnlopt0:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsis-base-java', 'libsis-base-jni', 'libsis-jhdf5-java', 'libsis-jhdf5-jni', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsodium23:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstaden-read14:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev:amd64', 'littler', 'media-types', 'megadepth', 'multiqc', 'ncbi-vdb-data', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.36', 'pigz', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-adal', 'python3-aiohttp', 'python3-aiosignal', 'python3-alabaster', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-async-timeout', 'python3-attr', 'python3-avro', 'python3-azure', 'python3-azure-storage', 'python3-babel', 'python3-bcrypt', 'python3-beniget', 'python3-blinker', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cryptography', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-dev', 'python3-distutils', 'python3-dnaio', 'python3-docutils', 'python3-fastjsonschema', 'python3-fonttools', 'python3-frozenlist', 'python3-fs', 'python3-future', 'python3-gast', 'python3-gi', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-idna', 'python3-imagesize', 'python3-isodate', 'python3-jinja2', 'python3-jmespath', 'python3-jsonschema', 'python3-jupyter-core', 'python3-jwt', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-marshmallow', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-msal', 'python3-msal-extensions', 'python3-msrest', 'python3-msrestazure', 'python3-multidict', 'python3-nacl', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-oauthlib', 'python3-packaging', 'python3-paramiko', 'python3-pbr', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plotly', 'python3-ply', 'python3-portalocker', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pysam', 'python3-pythran', 'python3-ratelimiter', 'python3-requests', 'python3-requests-oauthlib', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-s3transfer', 'python3-scipy', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-strictyaml', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-tqdm', 'python3-traitlets', 'python3-typing-extensions', 'python3-tz', 'python3-uamqp', 'python3-ufolib2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yarl', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', '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-blob', 'r-cran-boot', 'r-cran-brio', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-callr', '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-dbi', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', '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-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-maptools', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', '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-pkgload', 'r-cran-plogr', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-png', 'r-cran-polynom', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-processx', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-ps', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sp', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-testthat', '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-waldo', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xml-core', 'zip', 'zlib1g-dev:amd64', 'pigx-rnaseq'] 6m57.0s INFO: Running scripts post_remove 6m57.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_remove_exceptions'] 6m57.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_remove_exceptions'] 6m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cpp', 'cpp-12', 'cutadapt', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'g++', 'g++-12', 'gcc', 'gcc-12', 'gir1.2-glib-2.0:amd64', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libaec0:amd64', 'libapache-pom-java', 'libargs4j-java', 'libasan8:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgirepository-1.0-1:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnlopt0:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsis-base-java', 'libsis-base-jni', 'libsis-jhdf5-java', 'libsis-jhdf5-jni', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsodium23:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstaden-read14:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev:amd64', 'littler', 'media-types', 'megadepth', 'multiqc', 'ncbi-vdb-data', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.36', 'pigz', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-adal', 'python3-aiohttp', 'python3-aiosignal', 'python3-alabaster', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-async-timeout', 'python3-attr', 'python3-avro', 'python3-azure', 'python3-azure-storage', 'python3-babel', 'python3-bcrypt', 'python3-beniget', 'python3-blinker', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cryptography', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-dev', 'python3-distutils', 'python3-dnaio', 'python3-docutils', 'python3-fastjsonschema', 'python3-fonttools', 'python3-frozenlist', 'python3-fs', 'python3-future', 'python3-gast', 'python3-gi', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-idna', 'python3-imagesize', 'python3-isodate', 'python3-jinja2', 'python3-jmespath', 'python3-jsonschema', 'python3-jupyter-core', 'python3-jwt', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-marshmallow', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-msal', 'python3-msal-extensions', 'python3-msrest', 'python3-msrestazure', 'python3-multidict', 'python3-nacl', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-oauthlib', 'python3-packaging', 'python3-paramiko', 'python3-pbr', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plotly', 'python3-ply', 'python3-portalocker', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pysam', 'python3-pythran', 'python3-ratelimiter', 'python3-requests', 'python3-requests-oauthlib', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-s3transfer', 'python3-scipy', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-strictyaml', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-tqdm', 'python3-traitlets', 'python3-typing-extensions', 'python3-tz', 'python3-uamqp', 'python3-ufolib2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yarl', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', '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-blob', 'r-cran-boot', 'r-cran-brio', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-callr', '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-dbi', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', '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-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-maptools', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', '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-pkgload', 'r-cran-plogr', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-png', 'r-cran-polynom', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-processx', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-ps', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sp', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-testthat', '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-waldo', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 6m58.4s DUMP: (Reading database ... 6214 files and directories currently installed.) 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ignoring request to remove python3-deeptools which isn't installed dpkg: warning: ignoring request to remove python3-deeptoolsintervals which isn't installed dpkg: warning: ignoring request to remove python3-dev which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-dnaio which isn't installed dpkg: warning: ignoring request to remove python3-docutils 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-frozenlist which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-future which isn't installed dpkg: warning: ignoring request to remove python3-gast which isn't installed dpkg: warning: ignoring request to remove python3-gi 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-idna which isn't installed dpkg: warning: ignoring request to remove python3-imagesize which isn't installed dpkg: warning: ignoring request to remove python3-isodate which isn't installed dpkg: warning: ignoring request to remove python3-jinja2 which isn't installed dpkg: warning: ignoring request to remove python3-jmespath which isn't installed Purging configuration files for python3-jsonschema (4.10.3-1) ... dpkg: warning: ignoring request to remove python3-jupyter-core which isn't installed dpkg: warning: ignoring request to remove python3-jwt which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-lzstring which isn't installed dpkg: warning: ignoring request to remove python3-markdown which isn't installed dpkg: warning: ignoring request to remove python3-markdown-it which isn't installed dpkg: warning: ignoring request to remove python3-markupsafe which isn't installed dpkg: warning: ignoring request to remove python3-marshmallow which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-mdurl which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-msal which isn't installed dpkg: warning: ignoring request to remove python3-msal-extensions which isn't installed dpkg: warning: ignoring request to remove python3-msrest which isn't installed dpkg: warning: ignoring request to remove python3-msrestazure which isn't installed dpkg: warning: ignoring request to remove python3-multidict which isn't installed dpkg: warning: ignoring request to remove python3-nacl which isn't installed dpkg: warning: ignoring request to remove python3-nbformat which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-numpydoc which isn't installed dpkg: warning: ignoring request to remove python3-oauthlib which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-paramiko which isn't installed Purging configuration files for python3-pbr (5.10.0-2) ... dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-plotly which isn't installed dpkg: warning: ignoring request to remove python3-ply which isn't installed dpkg: warning: ignoring request to remove python3-portalocker which isn't installed dpkg: warning: ignoring request to remove python3-psutil which isn't installed dpkg: warning: ignoring request to remove python3-pulp which isn't installed dpkg: warning: ignoring request to remove python3-py which isn't installed dpkg: warning: ignoring request to remove python3-py2bit which isn't installed dpkg: warning: ignoring request to remove 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isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml which isn't installed dpkg: warning: ignoring request to remove python3-ruamel.yaml.clib which isn't installed dpkg: warning: ignoring request to remove python3-s3transfer which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-simplejson which isn't installed dpkg: warning: ignoring request to remove python3-six 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 dpkg: warning: ignoring request to remove python3-strictyaml which isn't installed Purging configuration files for python3-sympy (1.11.1-1) ... 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: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-traitlets which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-uamqp which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3-xopen which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3-yarl which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... Purging configuration files for r-base-core (4.2.2.20221110-2) ... dpkg: warning: ignoring request to remove r-bioc-annotate which isn't installed dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed 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-geneplotter 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-keggrest 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-s4vectors 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-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-blob 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-brio 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-callr 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-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-desc which isn't installed dpkg: warning: ignoring request to remove r-cran-diffobj 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-dplyr which isn't installed Purging configuration files for r-cran-dt (0.27+dfsg-1) ... 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-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-maptools 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-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-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-pkgload which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr 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-png 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-praise 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-processx 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-ps 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-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-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-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-rematch which isn't installed dpkg: warning: ignoring request to remove r-cran-rematch2 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 Purging configuration files for r-cran-rmarkdown (2.20+dfsg-1) ... dpkg: warning: ignoring request to remove r-cran-rpart which isn't installed dpkg: warning: ignoring request to remove r-cran-rprojroot which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite 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-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-sp 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-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-testthat 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-waldo 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-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 (8.2-1.3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove salmon which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for sgml-base (1.31) ... Purging configuration files for shared-mime-info (2.2-1) ... dpkg: warning: ignoring request to remove snakemake which isn't installed dpkg: warning: ignoring request to remove sphinx-common which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove trim-galore which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed Purging configuration files for xml-core (0.18+nmu1) ... dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 6m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'ca-certificates-java', 'coinor-cbc', 'coinor-libcbc3:amd64', 'coinor-libcgl1:amd64', 'coinor-libclp1:amd64', 'coinor-libcoinutils3v5:amd64', 'coinor-libosi1v5:amd64', 'cpp', 'cpp-12', 'cutadapt', 'default-jre', 'default-jre-headless', 'docutils-common', 'fastp', 'fastqc', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lyx', 'fonts-mathjax', 'g++', 'g++-12', 'gcc', 'gcc-12', 'gir1.2-glib-2.0:amd64', 'git', 'git-man', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'java-common', 'javascript-common', 'libaec0:amd64', 'libapache-pom-java', 'libargs4j-java', 'libasan8:amd64', 'libasound2:amd64', 'libasound2-data', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbigwig0:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcc1-0:amd64', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-math3-java', 'libcommons-parent-java', 'libcrypt-dev:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'liberror-perl', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfindbin-libs-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgif7:amd64', 'libgirepository-1.0-1:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libhtsjdk-java', 'libhwloc15:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libisal2', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-metadata', 'libjs-jquery-selectize.js', 'libjs-jquery-tablesorter', 'libjs-jquery-ui', 'libjs-json', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-sphinxdoc', 'libjs-twitter-bootstrap-datepicker', 'libjs-underscore', 'libjson-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmpc3:amd64', 'libmpfr6:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnlopt0:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libopenjp2-7:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.36:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsis-base-java', 'libsis-base-jni', 'libsis-jhdf5-java', 'libsis-jhdf5-jni', 'libsm6:amd64', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libsodium23:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstaden-read14:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libz3-4:amd64', 'linux-libc-dev:amd64', 'littler', 'media-types', 'megadepth', 'multiqc', 'ncbi-vdb-data', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.36', 'pigz', 'python-babel-localedata', 'python-matplotlib-data', 'python3', 'python3-adal', 'python3-aiohttp', 'python3-aiosignal', 'python3-alabaster', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-async-timeout', 'python3-attr', 'python3-avro', 'python3-azure', 'python3-azure-storage', 'python3-babel', 'python3-bcrypt', 'python3-beniget', 'python3-blinker', 'python3-boto3', 'python3-botocore', 'python3-brotli', 'python3-certifi', 'python3-cffi-backend:amd64', 'python3-chardet', 'python3-charset-normalizer', 'python3-click', 'python3-colorama', 'python3-coloredlogs', 'python3-colormath', 'python3-configargparse', 'python3-connection-pool', 'python3-contourpy', 'python3-cryptography', 'python3-cutadapt', 'python3-cycler', 'python3-dateutil', 'python3-datrie:amd64', 'python3-decorator', 'python3-deeptools', 'python3-deeptoolsintervals', 'python3-dev', 'python3-distutils', 'python3-dnaio', 'python3-docutils', 'python3-fastjsonschema', 'python3-fonttools', 'python3-frozenlist', 'python3-fs', 'python3-future', 'python3-gast', 'python3-gi', 'python3-git', 'python3-gitdb', 'python3-htseq', 'python3-humanfriendly', 'python3-idna', 'python3-imagesize', 'python3-isodate', 'python3-jinja2', 'python3-jmespath', 'python3-jsonschema', 'python3-jupyter-core', 'python3-jwt', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-lzstring', 'python3-markdown', 'python3-markdown-it', 'python3-markupsafe', 'python3-marshmallow', 'python3-matplotlib', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-msal', 'python3-msal-extensions', 'python3-msrest', 'python3-msrestazure', 'python3-multidict', 'python3-nacl', 'python3-nbformat', 'python3-networkx', 'python3-numpy', 'python3-numpydoc', 'python3-oauthlib', 'python3-packaging', 'python3-paramiko', 'python3-pbr', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-plotly', 'python3-ply', 'python3-portalocker', 'python3-psutil', 'python3-pulp', 'python3-py', 'python3-py2bit', 'python3-pybigwig', 'python3-pygments', 'python3-pyparsing', 'python3-pyrsistent:amd64', 'python3-pysam', 'python3-pythran', 'python3-ratelimiter', 'python3-requests', 'python3-requests-oauthlib', 'python3-retry', 'python3-rich', 'python3-rich-click', 'python3-roman', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib:amd64', 'python3-s3transfer', 'python3-scipy', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-smart-open', 'python3-smmap', 'python3-snowballstemmer', 'python3-spectra', 'python3-sphinx', 'python3-stopit', 'python3-strictyaml', 'python3-sympy', 'python3-tabulate', 'python3-tenacity', 'python3-throttler', 'python3-tk:amd64', 'python3-toposort', 'python3-tqdm', 'python3-traitlets', 'python3-typing-extensions', 'python3-tz', 'python3-uamqp', 'python3-ufolib2', 'python3-urllib3', 'python3-wrapt', 'python3-xopen', 'python3-yaml', 'python3-yarl', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', '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-blob', 'r-cran-boot', 'r-cran-brio', 'r-cran-broom', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-callr', '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-dbi', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', '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-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-maptools', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixmodels', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-miniui', 'r-cran-minqa', 'r-cran-modelmetrics', '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-pkgload', 'r-cran-plogr', 'r-cran-plotly', 'r-cran-plyr', 'r-cran-png', 'r-cran-polynom', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-proc', 'r-cran-processx', 'r-cran-prodlim', 'r-cran-progress', 'r-cran-progressr', 'r-cran-promises', 'r-cran-proxy', 'r-cran-ps', 'r-cran-purrr', 'r-cran-quantreg', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcppeigen', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-readxl', 'r-cran-recipes', 'r-cran-rematch', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rio', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rpart', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstatix', 'r-cran-sass', 'r-cran-scales', 'r-cran-shiny', 'r-cran-shinyjs', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sp', 'r-cran-sparsem', 'r-cran-squarem', 'r-cran-statmod', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-sys', 'r-cran-testthat', '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-waldo', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'r-cran-zip', 'readline-common', 'rpcsvc-proto', 'salmon', 'samtools', 'sensible-utils', 'sgml-base', 'shared-mime-info', 'snakemake', 'sphinx-common', 'tk8.6-blt2.5', 'trim-galore', 'ucf', 'unicode-data', 'unzip', 'x11-common', 'xdg-utils', 'xml-core', 'zip', 'zlib1g-dev:amd64'] 6m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', 'pigx-rnaseq'] 6m58.4s DUMP: dpkg: warning: ignoring request to remove pigx-rnaseq which isn't installed 6m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', 'pigx-rnaseq'] 6m58.4s INFO: Running scripts post_purge 6m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_purge_exceptions'] 6m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_purge_exceptions'] 6m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', '--pending'] 6m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--purge', '--pending'] 6m58.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--remove', '--pending'] 6m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg', '--remove', '--pending'] 6m58.5s INFO: Running scripts post_test 6m58.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_test_exceptions'] 6m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'tmp/scripts/post_test_exceptions'] 6m58.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 6m58.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 6m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-divert', '--list'] 6m58.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 6m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'dpkg-divert', '--list'] 6m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'clean'] 6m59.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip', 'apt-get', 'clean'] 6m59.0s DEBUG: Recording chroot state 6m60.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/shm'] 6m60.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/shm'] 6m60.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/console'] 6m60.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/console'] 6m60.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/ptmx'] 6m60.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/ptmx'] 6m60.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts'] 7m0.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/dev/pts'] 7m0.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/proc'] 7m0.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip/proc'] 7m0.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 7m0.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcd0u3cip'] 7m0.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpcd0u3cip 7m0.3s INFO: PASS: Upgrading between Debian distributions. 7m0.3s INFO: PASS: All tests. 7m0.3s INFO: piuparts run ends. ret=0 End: 2024-08-22 10:37:23 GMT