Start: 2024-03-27 23:31:25 GMT [stable] Package: trinityrnaseq Version: 2.11.0+dfsg-6 Installed-Size: 7229 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl, salmon, python3-numpy, ncbi-blast+, python3, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-fastcluster, liburi-perl, r-cran-ape, r-bioc-ctc, r-cran-gplots, r-bioc-biobase, r-bioc-goseq, r-bioc-tximport, python3-htseq, rna-star, gmap, hisat2, subread, kallisto, python3-hisat2, r-cran-argparse, r-cran-goplot, r-bioc-dexseq Recommends: trinityrnaseq-examples, r-cran-tidyverse, picard-tools, tabix Suggests: collectl, r-bioc-tximportdata Description: RNA-Seq De novo Assembly Homepage: https://trinityrnaseq.github.io/ Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.11.0+dfsg-6_amd64.deb Size: 1661784 MD5sum: 6a94a9b66756205b19e4a9a02aaa3de2 SHA256: 0e88995ee2e7aa9fe019d02ccaef378526350a03de667265c2baabc405513ea6 [testing] [sid] Package: trinityrnaseq Source: trinityrnaseq (2.15.1+dfsg-5) Version: 2.15.1+dfsg-5+b1 Installed-Size: 7456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description: RNA-Seq De novo Assembly Homepage: https://github.com/trinityrnaseq/trinityrnaseq Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.1+dfsg-5+b1_amd64.deb Size: 1720124 MD5sum: 091e1c91e745d24db55e1cc6ae5a33dc SHA256: 26095fdfb867b2e1976033be1d8a0e722cd129b4027f8f554bc381c88628464d Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt trinityrnaseq=2.15.1+dfsg-5+b1 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 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt trinityrnaseq=2.15.1+dfsg-5+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpizzr_c2w 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpizzr_c2w 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/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/tmpizzr_c2w/dev/pts'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/pts'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpizzr_c2w/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 0m1.8s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s INFO: Running scripts pre_test 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m4.7s DUMP: Package: trinityrnaseq Version: 2.11.0+dfsg-6 Installed-Size: 7229 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl, salmon, python3-numpy, ncbi-blast+, python3, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-fastcluster, liburi-perl, r-cran-ape, r-bioc-ctc, r-cran-gplots, r-bioc-biobase, r-bioc-goseq, r-bioc-tximport, python3-htseq, rna-star, gmap, hisat2, subread, kallisto, python3-hisat2, r-cran-argparse, r-cran-goplot, r-bioc-dexseq Recommends: trinityrnaseq-examples, r-cran-tidyverse, picard-tools, tabix Suggests: collectl, r-bioc-tximportdata Description-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: https://trinityrnaseq.github.io/ Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.11.0+dfsg-6_amd64.deb Size: 1661784 MD5sum: 6a94a9b66756205b19e4a9a02aaa3de2 SHA256: 0e88995ee2e7aa9fe019d02ccaef378526350a03de667265c2baabc405513ea6 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m4.7s INFO: apt-cache knows about the following packages: trinityrnaseq 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 0m4.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 0m4.8s DUMP: trinityrnaseq: Installed: (none) Candidate: 2.11.0+dfsg-6 Version table: 2.11.0+dfsg-6 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq'] 1m53.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato gmap hisat2 jaligner java-common jellyfish kallisto libapache-pom-java libasan6 libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libblas3 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcrypt-dev libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgdbm-compat4 libgdbm6 libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu67 libio-html-perl libio-socket-ssl-perl libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjung-free-java liblapack3 liblcms2-2 libldap-2.4-2 libllvm11 liblmdb0 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl-dev libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpixman-1-0 libpng16-16 libprotobuf23 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libstaden-read14 libstdc++-10-dev libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtirpc-dev libtk8.6 libtry-tiny-perl libtsan0 libubsan1 liburi-perl libvecmath-java libvulkan1 libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxml2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev littler media-types ncbi-blast+ ncbi-data netbase node-html5shiv openjdk-11-jre openjdk-11-jre-headless openssl parafly perl perl-modules-5.32 perl-openssl-defaults python3 python3-hisat2 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.9 python3.9-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-ctc r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-amap r-cran-ape r-cran-argparse r-cran-askpass r-cran-assertthat r-cran-bh r-cran-biasedurn r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-catools r-cran-cli r-cran-clipr r-cran-cluster r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-findpython r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-gdata r-cran-generics r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-goplot r-cran-gplots r-cran-gridextra r-cran-gtable r-cran-gtools r-cran-hms r-cran-httr r-cran-hwriter r-cran-isoband r-cran-jsonlite r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-reshape2 r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable readline-common rna-star rsem salmon samtools sensible-utils sphinx-rtd-theme-common subread transdecoder trimmomatic ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: bowtie-examples bowtie2-examples 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 manpages-dev libcommons-collections4-java-doc cups-common gdbm-l10n libdata-dump-perl liblcms2-utils libcrypt-ssleay-perl pciutils pcscd lm-sensors libstdc++-10-doc tcl8.6 tk8.6 libauthen-ntlm-perl nodejs libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python3-setuptools python3.9-venv python3.9-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-org.hs.eg.db r-cran-runit r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-rmarkdown r-bioc-affy r-cran-foreach r-cran-bbmisc r-bioc-variantannotation r-bioc-shortread r-cran-codetools r-cran-data.table r-bioc-bsgenome r-bioc-hdf5array r-bioc-delayedmatrixstats r-cran-pheatmap r-cran-pbapply r-cran-biocmanager r-bioc-rhdf5 r-bioc-ensembldb r-bioc-gviz r-bioc-annotationhub r-cran-ellipse r-bioc-sparsematrixstats r-cran-gee r-cran-expm r-cran-igraph clustalw muscle phyml t-coffee r-cran-covr r-cran-roxygen2 r-cran-rpart r-cran-htmlwidgets r-cran-prettycode r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg r-cran-viridis r-cran-bench r-cran-rmysql r-cran-broom r-cran-rpostgresql r-cran-unitizer r-cran-reticulate r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-sf r-cran-svglite r-cran-r.utils r-cran-forcats r-cran-lubridate r-cran-httpuv r-cran-magick r-cran-getopt r-cran-interp r-cran-gam r-cran-base64enc r-cran-doparallel r-cran-iterators r-cran-itertools r-cran-inline r-cran-gh r-cran-rvest r-cran-dichromat r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-mockery r-cran-usethis r-cran-formattable r-cran-htmltools r-cran-tidyr r-cran-zeallot r-cran-plm r-cran-zoo readline-doc r-bioc-ebseq cwltool collectl r-bioc-tximportdata Recommended packages: med-config bcftools alsa-ucm-conf alsa-topology-conf manpages manpages-dev libc-devtools dbus libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl libclone-perl javascript-common libldap-common libgpm2 publicsuffix libsasl2-modules mesa-vulkan-drivers | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libatk-wrapper-java-jni fonts-dejavu-extra r-recommended r-base-dev r-doc-html r-cran-runit r-cran-batchjobs r-cran-doparallel r-cran-batchtools r-cran-rmpi r-bioc-glmgampoi r-cran-class r-cran-knitr r-bioc-shortread r-bioc-org.hs.eg.db r-cran-cliapp r-cran-mockery r-cran-decor r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-data.table r-cran-testit r-cran-codetools r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-sodium r-cran-lubridate r-cran-domc r-cran-abind r-cran-rmarkdown r-cran-mockr r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets trinityrnaseq-examples r-cran-tidyverse picard-tools tabix libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato gmap hisat2 jaligner java-common jellyfish kallisto libapache-pom-java libasan6 libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libblas3 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcrypt-dev libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgdbm-compat4 libgdbm6 libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu67 libio-html-perl libio-socket-ssl-perl libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjung-free-java liblapack3 liblcms2-2 libldap-2.4-2 libllvm11 liblmdb0 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmd0 libmpdec3 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl-dev libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpixman-1-0 libpng16-16 libprotobuf23 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libstaden-read14 libstdc++-10-dev libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtirpc-dev libtk8.6 libtry-tiny-perl libtsan0 libubsan1 liburi-perl libvecmath-java libvulkan1 libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxml2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev littler media-types ncbi-blast+ ncbi-data netbase node-html5shiv openjdk-11-jre openjdk-11-jre-headless openssl parafly perl perl-modules-5.32 perl-openssl-defaults python3 python3-hisat2 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.9 python3.9-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-ctc r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-amap r-cran-ape r-cran-argparse r-cran-askpass r-cran-assertthat r-cran-bh r-cran-biasedurn r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-catools r-cran-cli r-cran-clipr r-cran-cluster r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-findpython r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-gdata r-cran-generics r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-goplot r-cran-gplots r-cran-gridextra r-cran-gtable r-cran-gtools r-cran-hms r-cran-httr r-cran-hwriter r-cran-isoband r-cran-jsonlite r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-reshape2 r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable readline-common rna-star rsem salmon samtools sensible-utils sphinx-rtd-theme-common subread transdecoder trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 387 newly installed, 0 to remove and 0 not upgraded. Need to get 525 MB of archives. After this operation, 1523 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 netbase all 6.3 [19.9 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libboost-filesystem1.74.0 amd64 1.74.0-9 [283 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libboost-thread1.74.0 amd64 1.74.0-9 [279 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libprotobuf23 amd64 3.12.4-1+deb11u1 [891 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 berkeley-express amd64 1.5.3+dfsg-1+b4 [228 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 bowtie amd64 1.3.0+dfsg1-1 [1638 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u3 [1305 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-1~deb11u1 [38.2 MB] Get:58 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 curl amd64 7.74.0-1.3+deb11u11 [271 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:92 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get:102 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.22+7-1~deb11u1 [194 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get:116 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 gmap amd64 2021-02-22+ds-1 [11.6 MB] Get:119 http://deb.debian.org/debian bullseye/main amd64 hisat2 amd64 2.2.1-2+b3 [3653 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 jaligner all 1.0+dfsg-7 [136 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u11 [344 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libjellyfish-2.0-2 amd64 2.3.0-10 [65.1 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 jellyfish amd64 2.3.0-10 [790 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 kallisto amd64 0.46.2+dfsg-2 [242 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get:128 http://deb.debian.org/debian bullseye/main amd64 libasan6 amd64 10.2.1-6 [2065 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libatomic1 amd64 10.2.1-6 [9008 B] Get:130 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 libitm1 amd64 10.2.1-6 [25.8 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 liblsan0 amd64 10.2.1-6 [828 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libtsan0 amd64 10.2.1-6 [2000 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 libubsan1 amd64 10.2.1-6 [777 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 libgcc-10-dev amd64 10.2.1-6 [2328 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 libc-dev-bin amd64 2.31-13+deb11u8 [276 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 linux-libc-dev amd64 5.10.209-2 [1698 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libtirpc-dev amd64 1.3.1-1+deb11u1 [191 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 libc6-dev amd64 2.31-13+deb11u8 [2361 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:147 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74.0 amd64 1.74.0-9 [264 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 libconcurrent-java all 1.3.4-4.1 [137 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 libcolt-free-java all 1.2.0+dfsg-7 [434 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 libcommons-collections4-java all 4.2-1 [662 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.14-1 [12.4 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 libhtscodecs2 amd64 0.5-3 [50.6 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libio-html-perl all 1.004-2 [16.1 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.28-1 [79.6 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 5 [7360 B] Get:176 http://deb.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-3+b1 [321 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 libjbzip2-java all 0.9.1-5 [42.6 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 libjemalloc2 amd64 5.2.1-3 [248 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 libjung-free-java all 2.0.1+dfsg-1.1 [999 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:187 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.20-1 [25.1 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 libwww-perl all 6.52-1 [192 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:194 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:195 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:196 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:197 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:198 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:199 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:200 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:201 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:202 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:203 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:204 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:205 http://deb.debian.org/debian bullseye/main amd64 libstaden-read14 amd64 1.14.13-4 [265 kB] Get:206 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:207 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:208 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:209 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:210 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:211 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:212 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:213 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:214 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:215 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:216 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:217 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:218 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:219 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:220 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get:221 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get:222 http://deb.debian.org/debian bullseye/main amd64 node-html5shiv all 3.7.3+dfsg-3 [12.9 kB] Get:223 http://deb.debian.org/debian bullseye/main amd64 parafly amd64 0.1.0-2 [17.1 kB] Get:224 http://deb.debian.org/debian bullseye/main amd64 python3-hisat2 all 2.2.1-2 [14.2 kB] Get:225 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:226 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:227 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:228 http://deb.debian.org/debian bullseye/main amd64 python3-htseq amd64 0.13.5-1 [221 kB] Get:229 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:230 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biobase amd64 2.50.0-1 [2229 kB] Get:231 http://deb.debian.org/debian bullseye/main amd64 r-bioc-s4vectors amd64 0.28.1-1 [2027 kB] Get:232 http://deb.debian.org/debian bullseye/main amd64 r-bioc-iranges amd64 2.24.1-1 [2202 kB] Get:233 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbi all 1.1.1-1 [619 kB] Get:234 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit amd64 4.0.4+dfsg-1 [422 kB] Get:235 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:236 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:237 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:238 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:239 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:240 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:241 http://deb.debian.org/debian bullseye/main amd64 r-cran-blob all 1.2.1-2 [49.1 kB] Get:242 http://deb.debian.org/debian bullseye/main amd64 r-cran-fastmap amd64 1.1.0-1 [64.7 kB] Get:243 http://deb.debian.org/debian bullseye/main amd64 r-cran-cachem amd64 1.0.3-1 [61.4 kB] Get:244 http://deb.debian.org/debian bullseye/main amd64 r-cran-memoise all 2.0.0-1 [52.9 kB] Get:245 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:246 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:247 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:248 http://deb.debian.org/debian bullseye/main amd64 r-cran-bh all 1.74.0-1 [5196 B] Get:249 http://deb.debian.org/debian bullseye/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:250 http://deb.debian.org/debian bullseye/main amd64 r-cran-rsqlite amd64 2.2.3-1 [1035 kB] Get:251 http://deb.debian.org/debian bullseye/main amd64 r-bioc-annotationdbi all 1.52.0-1 [4707 kB] Get:252 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml amd64 3.99-0.5-1 [1722 kB] Get:253 http://deb.debian.org/debian bullseye/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:254 http://deb.debian.org/debian bullseye/main amd64 r-cran-curl amd64 4.3+dfsg-1+b1 [151 kB] Get:255 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:256 http://deb.debian.org/debian bullseye/main amd64 r-cran-mime amd64 0.9-1+b1 [35.5 kB] Get:257 http://deb.debian.org/debian bullseye/main amd64 r-cran-sys amd64 3.4-1 [42.9 kB] Get:258 http://deb.debian.org/debian bullseye/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:259 http://deb.debian.org/debian bullseye/main amd64 r-cran-openssl amd64 1.4.3+dfsg-2 [376 kB] Get:260 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:261 http://deb.debian.org/debian bullseye/main amd64 r-cran-httr all 1.4.2-1 [478 kB] Get:262 http://deb.debian.org/debian bullseye/main amd64 r-bioc-annotate all 1.68.0+dfsg-1 [2103 kB] Get:263 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:264 http://deb.debian.org/debian bullseye/main amd64 r-cran-generics all 0.1.0-1 [73.5 kB] Get:265 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:266 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:267 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:268 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:269 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:270 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:271 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:272 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:273 http://deb.debian.org/debian bullseye/main amd64 r-cran-purrr amd64 0.3.4-1+b1 [398 kB] Get:274 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyselect amd64 1.1.0+dfsg-1 [192 kB] Get:275 http://deb.debian.org/debian bullseye/main amd64 r-cran-dplyr amd64 1.0.4-1 [1143 kB] Get:276 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:277 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbplyr all 2.1.0-1 [802 kB] Get:278 http://deb.debian.org/debian bullseye/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:279 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocfilecache all 1.14.0+dfsg-1 [289 kB] Get:280 http://deb.debian.org/debian bullseye/main amd64 r-cran-formatr all 1.7-2 [151 kB] Get:281 http://deb.debian.org/debian bullseye/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:282 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:283 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:284 http://deb.debian.org/debian bullseye/main amd64 r-cran-snow all 1:0.4.3-2 [109 kB] Get:285 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocparallel amd64 1.24.1-1 [1143 kB] Get:286 http://deb.debian.org/debian bullseye/main amd64 r-cran-hms all 1.0.0-1 [102 kB] Get:287 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:288 http://deb.debian.org/debian bullseye/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:289 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.5.3-1 [729 kB] Get:290 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringr all 1.4.0-2 [199 kB] Get:291 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml2 amd64 1.3.2-1+b1 [270 kB] Get:292 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biomart all 2.46.2+dfsg-1 [414 kB] Get:293 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get:294 http://deb.debian.org/debian bullseye/main amd64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get:295 http://deb.debian.org/debian bullseye/main amd64 r-bioc-xvector amd64 0.30.0-1 [620 kB] Get:296 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biostrings amd64 2.58.0-1 [14.2 MB] Get:297 http://deb.debian.org/debian bullseye/main amd64 r-cran-amap amd64 0.8-18-2+b1 [297 kB] Get:298 http://deb.debian.org/debian bullseye/main amd64 r-bioc-ctc all 1.64.0-1 [219 kB] Get:299 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:300 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:301 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrixstats amd64 0.58.0-3 [664 kB] Get:302 http://deb.debian.org/debian bullseye/main amd64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get:303 http://deb.debian.org/debian bullseye/main amd64 r-bioc-delayedarray amd64 0.16.1+dfsg-1 [1798 kB] Get:304 http://deb.debian.org/debian bullseye/main amd64 r-cran-bitops amd64 1.0-6-5 [23.6 kB] Get:305 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcurl amd64 1.98-1.2-1+b1 [787 kB] Get:306 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get:307 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get:308 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicranges amd64 1.42.0+dfsg-1 [1856 kB] Get:309 http://deb.debian.org/debian bullseye/main amd64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get:310 http://deb.debian.org/debian bullseye/main amd64 r-cran-survival amd64 3.2-7-1 [7631 kB] Get:311 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genefilter amd64 1.72.1-1 [1154 kB] Get:312 http://deb.debian.org/debian bullseye/main amd64 r-cran-locfit amd64 1.5-9.4-2+b1 [508 kB] Get:313 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:314 http://deb.debian.org/debian bullseye/main amd64 r-bioc-geneplotter all 1.68.0-1 [1551 kB] Get:315 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:316 http://deb.debian.org/debian bullseye/main amd64 r-cran-brio amd64 1.1.1-1 [31.7 kB] Get:317 http://deb.debian.org/debian bullseye/main amd64 r-cran-ps amd64 1.5.0-1 [277 kB] Get:318 http://deb.debian.org/debian bullseye/main amd64 r-cran-processx amd64 3.4.5-1 [295 kB] Get:319 http://deb.debian.org/debian bullseye/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:320 http://deb.debian.org/debian bullseye/main amd64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:321 http://deb.debian.org/debian bullseye/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:322 http://deb.debian.org/debian bullseye/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:323 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:324 http://deb.debian.org/debian bullseye/main amd64 r-cran-rstudioapi all 0.13-1 [262 kB] Get:325 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:326 http://deb.debian.org/debian bullseye/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:327 http://deb.debian.org/debian bullseye/main amd64 r-cran-diffobj amd64 0.3.2-1 [1069 kB] Get:328 http://deb.debian.org/debian bullseye/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:329 http://deb.debian.org/debian bullseye/main amd64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get:330 http://deb.debian.org/debian bullseye/main amd64 r-cran-testthat amd64 3.0.1-1 [1451 kB] Get:331 http://deb.debian.org/debian bullseye/main amd64 r-cran-isoband amd64 0.2.3-2 [2085 kB] Get:332 http://deb.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-53.1-1 [1115 kB] Get:333 http://deb.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.152-1 [2241 kB] Get:334 http://deb.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-34-1 [2998 kB] Get:335 http://deb.debian.org/debian bullseye/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:336 http://deb.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:337 http://deb.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 2.0-0+dfsg-1 [1684 kB] Get:338 http://deb.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:339 http://deb.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:340 http://deb.debian.org/debian bullseye/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:341 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get:342 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpparmadillo amd64 0.10.2.1.0-1 [1149 kB] Get:343 http://deb.debian.org/debian bullseye/main amd64 r-bioc-deseq2 amd64 1.30.1+dfsg-1 [1296 kB] Get:344 http://deb.debian.org/debian bullseye/main amd64 r-cran-hwriter all 1.3.2-4 [162 kB] Get:345 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhtslib amd64 1.22.0+dfsg-1 [1024 kB] Get:346 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rsamtools amd64 2.6.0-1 [3659 kB] Get:347 http://deb.debian.org/debian bullseye/main amd64 r-cran-statmod amd64 1.4.35-1 [255 kB] Get:348 http://deb.debian.org/debian bullseye/main amd64 r-bioc-dexseq all 1.36.0+dfsg-1 [449 kB] Get:349 http://deb.debian.org/debian bullseye/main amd64 r-bioc-limma amd64 3.46.0+dfsg-1 [1767 kB] Get:350 http://deb.debian.org/debian bullseye/main amd64 r-bioc-edger amd64 3.32.1+dfsg-1 [1077 kB] Get:351 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicalignments amd64 1.26.0-1 [2196 kB] Get:352 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rtracklayer amd64 1.50.0-1 [7467 kB] Get:353 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicfeatures all 1.42.1+dfsg-1 [1834 kB] Get:354 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genelendatabase all 1.26.0-1 [101 MB] Get:355 http://deb.debian.org/debian bullseye/main amd64 r-bioc-go.db all 3.12.1-1 [12.9 MB] Get:356 http://deb.debian.org/debian bullseye/main amd64 r-cran-biasedurn amd64 1.07-4 [300 kB] Get:357 http://deb.debian.org/debian bullseye/main amd64 r-bioc-goseq all 1.42.0-1 [1735 kB] Get:358 http://deb.debian.org/debian bullseye/main amd64 r-cran-plyr amd64 1.8.6-2 [830 kB] Get:359 http://deb.debian.org/debian bullseye/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:360 http://deb.debian.org/debian bullseye/main amd64 r-bioc-qvalue all 2.22.0-1 [2799 kB] Get:361 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rots amd64 1.18.0-1 [435 kB] Get:362 http://deb.debian.org/debian bullseye/main amd64 r-bioc-tximport all 1.18.0+dfsg-1 [86.2 kB] Get:363 http://deb.debian.org/debian bullseye/main amd64 r-cran-ape amd64 5.4-1-1 [2208 kB] Get:364 http://deb.debian.org/debian bullseye/main amd64 r-cran-findpython all 1.0.7-1 [23.6 kB] Get:365 http://deb.debian.org/debian bullseye/main amd64 r-cran-argparse all 2.0.3-1 [136 kB] Get:366 http://deb.debian.org/debian bullseye/main amd64 r-cran-catools amd64 1.18.1-1 [204 kB] Get:367 http://deb.debian.org/debian bullseye/main amd64 r-cran-clipr all 0.7.1-1 [50.7 kB] Get:368 http://deb.debian.org/debian bullseye/main amd64 r-cran-cluster amd64 2.1.1-1 [553 kB] Get:369 http://deb.debian.org/debian bullseye/main amd64 r-cran-cpp11 all 0.2.6-1 [144 kB] Get:370 http://deb.debian.org/debian bullseye/main amd64 r-cran-fastcluster amd64 1.1.25-3+b5 [184 kB] Get:371 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtools amd64 3.8.2-1+b1 [329 kB] Get:372 http://deb.debian.org/debian bullseye/main amd64 r-cran-gdata all 2.18.0-3 [1031 kB] Get:373 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggdendro all 0.1.22+dfsg-1 [143 kB] Get:374 http://deb.debian.org/debian bullseye/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:375 http://deb.debian.org/debian bullseye/main amd64 r-cran-goplot all 1.0.2-2 [2427 kB] Get:376 http://deb.debian.org/debian bullseye/main amd64 r-cran-kernsmooth amd64 2.23-18-1 [91.1 kB] Get:377 http://deb.debian.org/debian bullseye/main amd64 r-cran-gplots all 3.1.1-1 [607 kB] Get:378 http://deb.debian.org/debian bullseye/main amd64 r-cran-readr amd64 1.4.0-1 [753 kB] Get:379 http://deb.debian.org/debian bullseye/main amd64 rna-star amd64 2.7.8a+dfsg-2 [1279 kB] Get:380 http://deb.debian.org/debian bullseye/main amd64 rsem amd64 1.3.3+dfsg-1 [36.1 MB] Get:381 http://deb.debian.org/debian bullseye/main amd64 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get:382 http://deb.debian.org/debian bullseye/main amd64 salmon amd64 1.4.0+ds1-1+b4 [2221 kB] Get:383 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:384 http://deb.debian.org/debian bullseye/main amd64 subread amd64 2.0.1+dfsg-1 [667 kB] Get:385 http://deb.debian.org/debian bullseye/main amd64 transdecoder all 5.0.1-3 [187 kB] Get:386 http://deb.debian.org/debian bullseye/main amd64 trimmomatic all 0.39+dfsg-2 [758 kB] Get:387 http://deb.debian.org/debian bullseye/main amd64 trinityrnaseq amd64 2.11.0+dfsg-6 [1662 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 525 MB in 35s (15.1 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6674 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.2+20201114-2+deb11u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.34.1-3_amd64.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9403 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... 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Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../025-libfreetype6_2.10.4+dfsg-1+deb11u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../026-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../027-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../028-libfontconfig1_2.13.1-4.2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-4.2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../029-libnspr4_2%3a4.29-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.29-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../030-libnss3_2%3a3.61-1+deb11u3_amd64.deb ... Unpacking libnss3:amd64 (2:3.61-1+deb11u3) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../031-libasound2-data_1.2.4-1.1_all.deb ... Unpacking libasound2-data (1.2.4-1.1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../032-libasound2_1.2.4-1.1_amd64.deb ... Unpacking libasound2:amd64 (1.2.4-1.1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../033-libglib2.0-0_2.66.8-1+deb11u1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.8-1+deb11u1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../034-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../035-libharfbuzz0b_2.7.4-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (2.7.4-1) ... Selecting previously unselected package libpcsclite1:amd64. 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Preparing to unpack .../041-libsasl2-2_2.1.27+dfsg-2.1+deb11u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../042-libldap-2.4-2_2.4.57+dfsg-3+deb11u1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../043-libnghttp2-14_1.43.0-1+deb11u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../044-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../045-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../046-libssh2-1_1.9.0-2_amd64.deb ... 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Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+dfsg-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 liblsan0:amd64 (10.2.1-6) ... Setting up libitm1:amd64 (10.2.1-6) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0-9) ... Setting up libtsan0:amd64 (10.2.1-6) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up parafly (0.1.0-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libgcc-10-dev:amd64 (10.2.1-6) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libavahi-common3:amd64 (0.8-5+deb11u2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u11) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up libcommons-collections4-java (4.2-1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up berkeley-express (1.5.3+dfsg-1+b4) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Setting up libc6-dev:amd64 (2.31-13+deb11u8) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up curl (7.74.0-1.3+deb11u11) ... Setting up libstaden-read14:amd64 (1.14.13-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up libxcb-dri3-0:amd64 (1.14-3) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Setting up libhts3:amd64 (1.11-4) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libstdc++-10-dev:amd64 (10.2.1-6) ... Setting up libboost1.74-dev:amd64 (1.74.0-9) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up rna-star (2.7.8a+dfsg-2) ... Setting up samtools (1.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up salmon (1.4.0+ds1-1+b4) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up jellyfish (2.3.0-10) ... Setting up libio-html-perl (1.004-2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up kallisto (0.46.2+dfsg-2) ... Setting up liburi-perl (5.08-1) ... Setting up gmap (2021-02-22+ds-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up r-cran-bh (1.74.0-1) ... Setting up libhttp-date-perl (6.05-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnet-http-perl (6.20-1) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up hisat2 (2.2.1-2+b3) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up libhttp-message-perl (6.28-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-hisat2 (2.2.1-2) ... Setting up bowtie (1.3.0+dfsg1-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-biasedurn (1.07-4) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up r-cran-formatr (1.7-2) ... Setting up r-cran-xml (3.99-0.5-1) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up r-cran-locfit (1.5-9.4-2+b1) ... Setting up r-cran-cluster (2.1.1-1) ... Setting up rsem (1.3.3+dfsg-1) ... Setting up r-cran-statmod (1.4.35-1) ... Setting up r-cran-clipr (0.7.1-1) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-fastcluster (1.1.25-3+b5) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up python3-htseq (0.13.5-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.4-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up transdecoder (5.0.1-3) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-curl (4.3+dfsg-1+b1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-matrixstats (0.58.0-3) ... Setting up r-cran-findpython (1.0.7-1) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-cran-amap (0.8-18-2+b1) ... Setting up r-bioc-matrixgenerics (1.2.1-4) ... Setting up r-cran-sys (3.4-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-mime (0.9-1+b1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-generics (0.1.0-1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-ape (5.4-1-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-xml2 (1.3.2-1+b1) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-dbi (1.1.1-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up r-cran-gtools (3.8.2-1+b1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-bit (4.0.4+dfsg-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-bitops (1.0-6-5) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.0-1) ... Setting up r-bioc-biobase (2.50.0-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-stringi (1.5.3-1) ... Setting up r-cran-hwriter (1.3.2-4) ... Setting up r-bioc-rots (1.18.0-1) ... Setting up r-cran-cpp11 (0.2.6-1) ... Setting up r-cran-plyr (1.8.6-2) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-gridextra (2.3-3) ... Setting up r-bioc-limma (3.46.0+dfsg-1) ... Setting up r-cran-purrr (0.3.4-1+b1) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-bioc-tximport (1.18.0+dfsg-1) ... Setting up r-cran-kernsmooth (2.23-18-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-cran-cachem (1.0.3-1) ... Setting up r-cran-catools (1.18.1-1) ... Setting up r-cran-rcpparmadillo (0.10.2.1.0-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up r-bioc-ctc (1.64.0-1) ... Setting up r-cran-argparse (2.0.3-1) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... Setting up r-cran-gdata (2.18.0-3) ... Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-openssl (1.4.3+dfsg-2) ... Setting up r-cran-stringr (1.4.0-2) ... Setting up r-bioc-biocparallel (1.24.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-bioc-edger (3.32.1+dfsg-1) ... Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-survival (3.2-7-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-httr (1.4.2-1) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-memoise (2.0.0-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-gplots (3.1.1-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-tidyselect (1.1.0+dfsg-1) ... Setting up r-cran-hms (1.0.0-1) ... Setting up r-cran-blob (1.2.1-2) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-cran-dplyr (1.0.4-1) ... Setting up r-cran-dbplyr (2.1.0-1) ... Setting up r-cran-rsqlite (2.2.3-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-bioc-biocfilecache (1.14.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.52.0-1) ... Setting up r-bioc-go.db (3.12.1-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-bioc-annotate (1.68.0+dfsg-1) ... Setting up r-cran-readr (1.4.0-1) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-bioc-biomart (2.46.2+dfsg-1) ... Setting up r-bioc-genefilter (1.72.1-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Setting up r-bioc-geneplotter (1.68.0-1) ... Setting up r-bioc-rtracklayer (1.50.0-1) ... Setting up r-bioc-genomicfeatures (1.42.1+dfsg-1) ... Setting up r-bioc-genelendatabase (1.26.0-1) ... Setting up r-bioc-goseq (1.42.0-1) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up r-bioc-deseq2 (1.30.1+dfsg-1) ... Setting up r-bioc-dexseq (1.36.0+dfsg-1) ... Setting up r-cran-ggdendro (0.1.22+dfsg-1) ... Setting up r-bioc-qvalue (2.22.0-1) ... Setting up r-cran-goplot (1.0.2-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up libwww-perl (6.52-1) ... Setting up openjdk-11-jre-headless:amd64 (11.0.22+7-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libconcurrent-java (1.3.4-4.1) ... Setting up openjdk-11-jre:amd64 (11.0.22+7-1~deb11u1) ... Setting up jaligner (1.0+dfsg-7) ... Setting up default-jre (2:1.11-72) ... Setting up libcolt-free-java (1.2.0+dfsg-7) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up trimmomatic (0.39+dfsg-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libjung-free-java (2.0.1+dfsg-1.1) ... Setting up trinityrnaseq (2.11.0+dfsg-6) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 1m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq'] 1m53.3s INFO: Running scripts post_install 1m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 1m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 1m53.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 1m54.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 1m54.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpizzr_c2w to testing 1m54.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 1m54.9s INFO: Running scripts pre_distupgrade 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_exceptions'] 1m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_exceptions'] 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m54.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m54.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 1m58.2s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8786 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 2s (6333 kB/s) Reading package lists... 1m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 1m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 3m56.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fonts-font-awesome fonts-lato gcc-11-base libasan6 libbamtools2.5.1 libcolt-free-java libconcurrent-java libgcc-10-dev libicu67 libldap-2.4-2 libllvm11 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libprotobuf23 libpython3.9-minimal libpython3.9-stdlib libstdc++-10-dev libtiff5 libtsan0 libvecmath-java libvulkan1 libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 python3.9 python3.9-minimal sphinx-rtd-theme-common Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1 libtbb2 The following NEW packages will be installed: adwaita-icon-theme at-spi2-common gcc-11-base gcc-12-base gtk-update-icon-cache hicolor-icon-theme libasan8 libatinject-jsr330-api-java libatk1.0-0 libbamtools2.5.2 libcap2 libclone-perl liberror-prone-java libffi8 libfile-find-rule-perl libgcc-12-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgtk2.0-0 libgtk2.0-common libguava-java libhwloc15 libicu72 libjsr305-java libldap-2.5-0 liblerc4 libllvm15 libmbedcrypto7 libmbedtls14 libmbedx509-1 libnumber-compare-perl libperl5.36 libprotobuf32 libpython3.11-minimal libpython3.11-stdlib libregexp-ipv6-perl libsemanage2 libsepol2 libssl3 libstdc++-12-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libtext-glob-perl libtiff6 libtsan2 libuv1 libwebp7 libxcb-randr0 libxcomposite1 libxcursor1 libxinerama1 libxrandr2 openjdk-17-jre openjdk-17-jre-headless perl-modules-5.36 python3.11 python3.11-minimal r-bioc-biocio r-bioc-keggrest r-cran-codetools r-cran-filelock r-cran-fs r-cran-png r-cran-restfulr r-cran-rjson r-cran-tzdb r-cran-vroom r-cran-yaml rpcsvc-proto shared-mime-info usrmerge util-linux-extra The following packages will be upgraded: adduser apt base-files base-passwd bash berkeley-express bowtie bowtie2 bsdutils ca-certificates ca-certificates-java coreutils curl dash debconf debian-archive-keyring debianutils default-jre default-jre-headless diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gmap gpgv grep gzip hisat2 hostname init-system-helpers jaligner java-common jellyfish kallisto libacl1 libapache-pom-java libapt-pkg6.0 libasan6 libasound2 libasound2-data libatomic1 libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libblkid1 libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcom-err2 libcommons-parent-java libconcurrent-java libcrypt-dev libcrypt1 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdb5.3 libdbus-1-3 libdebconfclient0 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libext2fs2 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3 libhtscodecs2 libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libidn2-0 libio-html-perl libio-socket-ssl-perl libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblsan0 liblwp-mediatypes-perl liblz4-1 liblzma5 libmd0 libmount1 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnettle8 libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcre2-8-0 libpcre3 libpcsclite1 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsensors-config libsensors5 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libstaden-read14 libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtry-tiny-perl libtsan0 libubsan1 libudev1 libunistring2 liburi-perl libuuid1 libvulkan1 libwww-perl libx11-6 libx11-data libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxdamage1 libxext6 libxfixes3 libxft2 libxi6 libxml2 libxrender1 libxt6 libxtst6 libxxhash0 libz3-4 libzstd1 linux-libc-dev littler login logsave lsb-base mawk media-types mount ncbi-blast+ ncbi-data ncurses-base ncurses-bin netbase node-html5shiv openssl parafly passwd perl perl-base perl-openssl-defaults python3 python3-hisat2 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-ctc r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-amap r-cran-ape r-cran-argparse r-cran-bh r-cran-biasedurn r-cran-bit r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-catools r-cran-cli r-cran-clipr r-cran-cluster r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-formatr r-cran-gdata r-cran-generics r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-gplots r-cran-gtable r-cran-gtools r-cran-hms r-cran-httr r-cran-hwriter r-cran-isoband r-cran-jsonlite r-cran-kernsmooth r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-processx r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 readline-common rna-star rsem salmon samtools sed sensible-utils sphinx-rtd-theme-common subread sysvinit-utils tar transdecoder tzdata ucf unzip util-linux x11-common zip zlib1g zlib1g-dev 409 upgraded, 73 newly installed, 2 to remove and 0 not upgraded. Need to get 590 MB of archives. After this operation, 572 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u5 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u4 [1897 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u4 [45.4 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u4 [2748 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u4 [606 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:14 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:27 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.76-1 [1930 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+b1 [147 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+b1 [166 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+b1 [107 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+b1 [111 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+b1 [1177 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2+deb12u1 [836 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B] Get:48 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b2 [1491 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+b1 [94.4 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.22-1~deb12u1 [331 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.22-1~deb12u1 [108 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u2 [1404 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+b3 [46.6 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B] Get:94 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:96 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:97 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 37~deb12u1 [13.3 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 python3-htseq amd64 1.99.2-1+b3 [268 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:118 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u5 [385 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+b1 [28.8 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:143 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-21 [240 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libjemalloc2 amd64 5.3.0-1 [275 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libstaden-read14 amd64 1.14.15-1 [265 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 salmon amd64 1.10.1+ds1-1+b1 [3297 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libtbbmalloc2 amd64 2021.8.0-2 [46.3 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libtbbbind-2-5 amd64 2021.8.0-2 [13.5 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 libtbb12 amd64 2021.8.0-2 [79.1 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+b1 [134 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2024a-0+deb12u1 [297 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-4 [149 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libprotobuf32 amd64 3.21.12-3 [932 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 berkeley-express amd64 1.5.3+dfsg-3+b1 [226 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 bowtie amd64 1.3.1-1+b1 [1627 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 curl amd64 7.88.1-10+deb12u5 [315 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u5 [390 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get:198 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.10+7-1~deb12u1 [43.7 MB] Get:215 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get:216 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get:217 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:246 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get:257 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.10+7-1~deb12u1 [184 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 gcc-11-base amd64 11.3.0-12 [38.4 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 gmap amd64 2021-12-17+ds-3 [11.3 MB] Get:277 http://deb.debian.org/debian bookworm/main amd64 hisat2 amd64 2.2.1-4+b2 [3658 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 jaligner all 1.0+dfsg-10 [132 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 jellyfish amd64 2.3.0-15+b3 [789 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 libjellyfish-2.0-2 amd64 2.3.0-15+b3 [63.2 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 kallisto amd64 0.48.0+dfsg-3 [275 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get:283 http://deb.debian.org/debian bookworm/main amd64 libasan6 amd64 11.3.0-12 [2050 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:286 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:287 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:289 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:291 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:295 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:296 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:297 http://deb.debian.org/debian bookworm/main amd64 libconcurrent-java all 1.3.4-6 [140 kB] Get:298 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:299 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:300 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get:301 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:302 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:303 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:304 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:305 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:306 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:307 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:308 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:309 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get:310 http://deb.debian.org/debian bookworm/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:311 http://deb.debian.org/debian bookworm/main amd64 libjung-free-java all 2.1.1-2 [1477 kB] Get:312 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:313 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:314 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:315 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:316 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:317 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:318 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:319 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:320 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:321 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:322 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:323 http://deb.debian.org/debian bookworm/main amd64 libtsan0 amd64 11.3.0-12 [2016 kB] Get:324 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get:325 http://deb.debian.org/debian bookworm/main amd64 libvulkan1 amd64 1.3.239.0-1 [116 kB] Get:326 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get:327 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:328 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:329 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:330 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:331 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:332 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:333 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:334 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:335 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:336 http://deb.debian.org/debian bookworm/main amd64 parafly amd64 0.1.0-4 [17.5 kB] Get:337 http://deb.debian.org/debian bookworm/main amd64 python3-hisat2 all 2.2.1-4 [13.9 kB] Get:338 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:339 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:340 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:341 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:342 http://deb.debian.org/debian bookworm/main amd64 r-bioc-tximport all 1.26.1+dfsg-1 [87.9 kB] Get:343 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:344 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:345 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:346 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:347 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:348 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:349 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:350 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:351 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:352 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:353 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:354 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:355 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:356 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:357 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:358 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:359 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:360 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:361 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:362 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:363 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:364 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:365 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:366 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:367 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:368 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:369 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:370 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:371 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:372 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:373 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rots amd64 1.26.0-1 [382 kB] Get:374 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:375 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:376 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:377 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:378 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:379 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:380 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:381 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:382 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:383 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:384 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:385 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:386 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:387 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:388 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:389 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:390 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:391 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:392 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:393 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:394 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:395 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:396 http://deb.debian.org/debian bookworm/main amd64 r-bioc-qvalue all 2.30.0-1 [2797 kB] Get:397 http://deb.debian.org/debian bookworm/main amd64 r-bioc-limma amd64 3.54.1+dfsg-1 [1768 kB] Get:398 http://deb.debian.org/debian bookworm/main amd64 r-cran-biasedurn amd64 2.0.9-1 [275 kB] Get:399 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:400 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:401 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:402 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:403 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:404 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:405 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:406 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:407 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:408 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:409 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:410 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:411 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:412 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:413 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:414 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:415 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:416 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:417 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:418 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:419 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:420 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:421 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:422 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:423 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:424 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:425 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:426 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genelendatabase all 1.34.0-1 [101 MB] Get:427 http://deb.debian.org/debian bookworm/main amd64 r-bioc-go.db all 3.16.0-1 [12.4 MB] Get:428 http://deb.debian.org/debian bookworm/main amd64 r-bioc-goseq all 1.50.0-1 [1735 kB] Get:429 http://deb.debian.org/debian bookworm/main amd64 r-bioc-geneplotter all 1.76.0-1 [1488 kB] Get:430 http://deb.debian.org/debian bookworm/main amd64 r-cran-survival amd64 3.5-3-1 [5910 kB] Get:431 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genefilter amd64 1.80.3-1 [1042 kB] Get:432 http://deb.debian.org/debian bookworm/main amd64 r-cran-locfit amd64 1.5-9.7-1 [507 kB] Get:433 http://deb.debian.org/debian bookworm/main amd64 r-bioc-edger amd64 3.40.2+dfsg-1 [1093 kB] Get:434 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpparmadillo amd64 0.12.0.1.0-1 [841 kB] Get:435 http://deb.debian.org/debian bookworm/main amd64 r-bioc-deseq2 amd64 1.38.3+dfsg-1 [1288 kB] Get:436 http://deb.debian.org/debian bookworm/main amd64 r-cran-hwriter all 1.3.2.1-1 [110 kB] Get:437 http://deb.debian.org/debian bookworm/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:438 http://deb.debian.org/debian bookworm/main amd64 r-bioc-dexseq all 1.44.0+dfsg-1 [455 kB] Get:439 http://deb.debian.org/debian bookworm/main amd64 r-cran-amap amd64 0.8-19-1 [242 kB] Get:440 http://deb.debian.org/debian bookworm/main amd64 r-bioc-ctc all 1.72.0-1 [137 kB] Get:441 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotate all 1.76.0+dfsg-1 [1727 kB] Get:442 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:443 http://deb.debian.org/debian bookworm/main amd64 r-cran-ape amd64 5.7-1 [2884 kB] Get:444 http://deb.debian.org/debian bookworm/main amd64 r-cran-argparse all 2.2.2+dfsg-1 [143 kB] Get:445 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:446 http://deb.debian.org/debian bookworm/main amd64 r-cran-brio amd64 1.1.3-1+b1 [35.5 kB] Get:447 http://deb.debian.org/debian bookworm/main amd64 r-cran-ps amd64 1.7.2-1 [308 kB] Get:448 http://deb.debian.org/debian bookworm/main amd64 r-cran-processx amd64 3.8.0-1 [339 kB] Get:449 http://deb.debian.org/debian bookworm/main amd64 r-cran-callr all 3.7.3-2 [426 kB] Get:450 http://deb.debian.org/debian bookworm/main amd64 r-cran-catools amd64 1.18.2-1+b1 [204 kB] Get:451 http://deb.debian.org/debian bookworm/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:452 http://deb.debian.org/debian bookworm/main amd64 r-cran-cluster amd64 2.1.4-1 [567 kB] Get:453 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:454 http://deb.debian.org/debian bookworm/main amd64 r-cran-rprojroot all 2.0.3-1 [119 kB] Get:455 http://deb.debian.org/debian bookworm/main amd64 r-cran-desc all 1.4.2-1 [348 kB] Get:456 http://deb.debian.org/debian bookworm/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB] Get:457 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:458 http://deb.debian.org/debian bookworm/main amd64 r-cran-evaluate all 0.20-1 [85.9 kB] Get:459 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastcluster amd64 1.2.3-2 [188 kB] Get:460 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:461 http://deb.debian.org/debian bookworm/main amd64 r-cran-fs amd64 1.6.1+dfsg-1 [226 kB] Get:462 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtools amd64 3.9.4-1 [359 kB] Get:463 http://deb.debian.org/debian bookworm/main amd64 r-cran-gdata all 2.18.0.1-1 [1033 kB] Get:464 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggdendro all 0.1.23+dfsg-1 [143 kB] Get:465 http://deb.debian.org/debian bookworm/main amd64 r-cran-kernsmooth amd64 2.23-20-1 [91.5 kB] Get:466 http://deb.debian.org/debian bookworm/main amd64 r-cran-gplots all 3.1.3-1 [607 kB] Get:467 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:468 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgbuild all 1.4.0-1 [187 kB] Get:469 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgload all 1.3.2-1 [206 kB] Get:470 http://deb.debian.org/debian bookworm/main amd64 r-cran-plyr amd64 1.8.8-1 [832 kB] Get:471 http://deb.debian.org/debian bookworm/main amd64 r-cran-tzdb amd64 0.3.0-1 [484 kB] Get:472 http://deb.debian.org/debian bookworm/main amd64 r-cran-vroom amd64 1.6.1-1 [842 kB] Get:473 http://deb.debian.org/debian bookworm/main amd64 r-cran-readr amd64 2.1.4-1 [776 kB] Get:474 http://deb.debian.org/debian bookworm/main amd64 r-cran-rstudioapi all 0.14-1 [281 kB] Get:475 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:476 http://deb.debian.org/debian bookworm/main amd64 r-cran-waldo all 0.4.0-1 [116 kB] Get:477 http://deb.debian.org/debian bookworm/main amd64 r-cran-testthat amd64 3.1.6-1 [1545 kB] Get:478 http://deb.debian.org/debian bookworm/main amd64 rna-star amd64 2.7.10b+dfsg-2+b2 [3447 kB] Get:479 http://deb.debian.org/debian bookworm/main amd64 rsem amd64 1.3.3+dfsg-2+b1 [36.1 MB] Get:480 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get:481 http://deb.debian.org/debian bookworm/main amd64 subread amd64 2.0.3+dfsg-1 [770 kB] Get:482 http://deb.debian.org/debian bookworm/main amd64 transdecoder all 5.0.1-5 [187 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 590 MB in 23s (25.2 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 ... 47196 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u5_amd64.deb ... Unpacking base-files (12.4+deb12u5) over (11.1+deb11u9) ... Setting up base-files (12.4+deb12u5) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 47196 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) over (1:4.4.18-4) ... Preparing to unpack .../libc6-dev_2.36-9+deb12u4_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Replacing files in old package libc6:amd64 (2.31-13+deb11u8) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u4_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../rpcsvc-proto_1.4.3-1_amd64.deb ... Unpacking rpcsvc-proto (1.4.3-1) ... Preparing to unpack .../libaudit-common_1%3a3.0.9-1_all.deb ... Unpacking libaudit-common (1:3.0.9-1) over (1:3.0-2) ... Setting up libaudit-common (1:3.0.9-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47206 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u4_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Setting up libc6:amd64 (2.36-9+deb12u4) ... (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 ... 47191 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u4_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Setting up libc-bin (2.36-9+deb12u4) ... (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 ... 47191 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-1+b3_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.3-1+b3) over (0.7.9-2.2+b1) ... Setting up libcap-ng0:amd64 (0.8.3-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47193 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.9-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.0.9-1) over (1:3.0-2) ... Setting up libaudit1:amd64 (1:3.0.9-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47193 files and directories currently installed.) Preparing to unpack .../0-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) over (3.75-1+b1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../1-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Preparing to unpack .../2-perl-openssl-defaults_7+b1_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b1) over (5) ... Preparing to unpack .../3-libnet-ssleay-perl_1.92-2+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.92-2+b1) over (1.88-3+b1) ... Preparing to unpack .../4-perl_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl (5.36.0-7+deb12u1) over (5.32.1-4+deb11u3) ... Selecting previously unselected package perl-modules-5.36. Preparing to unpack .../5-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Preparing to unpack .../6-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) over (1.19-2) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../7-libperl5.36_5.36.0-7+deb12u1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7+deb12u1) ... Preparing to unpack .../8-perl-base_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl-base (5.36.0-7+deb12u1) over (5.32.1-4+deb11u3) ... Setting up perl-base (5.36.0-7+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 ... 49133 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5+b1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5+b1) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49134 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-1) over (5.3.28+dfsg1-0.8) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49134 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) over (1.19-2) ... Preparing to unpack .../zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-2+deb11u2) ... Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1) over (1:1.2.11.dfsg-2+deb11u2) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49137 files and directories currently installed.) Preparing to unpack .../libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) over (3.20-4) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Preparing to unpack .../liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) over (5.08-1) ... Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.77) ... Setting up debconf (1.5.82) ... (Reading database ... (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 ... 49145 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam0g:amd64 (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam0g:amd64 (1.5.2-6+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49145 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.33-2) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... (Reading database ... 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Preparing to unpack .../util-linux-extra_2.38.1-5+b1_amd64.deb ... Unpacking util-linux-extra (2.38.1-5+b1) ... Setting up util-linux-extra (2.38.1-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49223 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.4.1-0.2) over (5.2.5-2.1~deb11u1) ... Setting up liblzma5:amd64 (5.4.1-0.2) ... (Reading database ... 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(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 ... 49223 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.22_amd64.deb ... Unpacking dpkg (1.21.22) over (1.20.13) ... Setting up dpkg (1.21.22) ... Installing new version of config file /etc/cron.daily/dpkg ... (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 ... 49225 files and directories currently installed.) Preparing to unpack .../archives/lsb-base_11.6_all.deb ... Unpacking lsb-base (11.6) over (11.1.0) ... Preparing to unpack .../sysvinit-utils_3.06-4_amd64.deb ... Unpacking sysvinit-utils (3.06-4) over (2.96-7+deb11u1) ... Setting up sysvinit-utils (3.06-4) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49230 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1_amd64.deb ... Unpacking coreutils (9.1-1) over (8.32-4+b1) ... Setting up coreutils (9.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49229 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-2_amd64.deb ... Unpacking dash (0.5.12-2) over (0.5.11+git20200708+dd9ef66-5) ... Setting up dash (0.5.12-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49230 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-4_amd64.deb ... Unpacking diffutils (1:3.8-4) over (1:3.7-5) ... Setting up diffutils (1:3.8-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49230 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-4_amd64.deb ... Unpacking findutils (4.9.0-4) over (4.8.0-1) ... Setting up findutils (4.9.0-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49230 files and directories currently installed.) Preparing to unpack .../archives/grep_3.8-5_amd64.deb ... Unpacking grep (3.8-5) over (3.6-1+deb11u1) ... Setting up grep (3.8-5) ... (Reading database ... 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Setting up libtinfo6:amd64 (6.4-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49230 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4-4_amd64.deb ... Unpacking ncurses-bin (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4-4) ... (Reading database ... (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 ... 49230 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_amd64.deb ... Unpacking sed (4.9-1) over (4.7-1) ... Setting up sed (4.9-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49233 files and directories currently installed.) Preparing to unpack .../libstdc++6_12.2.0-14_amd64.deb ... Unpacking libstdc++6:amd64 (12.2.0-14) over (10.2.1-6) ... Setting up libstdc++6:amd64 (12.2.0-14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49233 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-1_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1) over (1.9.3-2) ... Setting up liblz4-1:amd64 (1.9.4-1) ... Selecting previously unselected package libcap2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49233 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-4_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49241 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.22-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.22-1~deb12u1) over (247.3-7+deb11u4) ... Setting up libsystemd0:amd64 (252.22-1~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 ... 49242 files and directories currently installed.) Preparing to unpack .../libudev1_252.22-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.22-1~deb12u1) over (247.3-7+deb11u4) ... Setting up libudev1:amd64 (252.22-1~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 ... 49243 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.1-1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.1-1) over (0.8.0-2) ... Setting up libxxhash0:amd64 (0.8.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49243 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.6.1_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.6.1) over (2.2.4) ... Setting up libapt-pkg6.0:amd64 (2.6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49243 files and directories currently installed.) Preparing to unpack .../libnettle8_3.8.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libnettle8:amd64 (3.8.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49243 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.8.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libhogweed6:amd64 (3.8.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49243 files and directories currently installed.) Preparing to unpack .../libunistring2_1.0-2_amd64.deb ... Unpacking libunistring2:amd64 (1.0-2) over (0.9.10-4) ... Setting up libunistring2:amd64 (1.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49243 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.3-1+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.3-1+b1) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.3-1+b1) ... Selecting previously unselected package libffi8:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49245 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49250 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.1-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.24.1-2) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.24.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49250 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49250 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u2_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u2) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u2) ... (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 ... 49252 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1_all.deb ... Unpacking libsemanage-common (3.4-1) over (3.1-1) ... Setting up libsemanage-common (3.4-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49252 files and directories currently installed.) Preparing to unpack .../libsepol2_3.4-2.1_amd64.deb ... Unpacking libsepol2:amd64 (3.4-2.1) ... Setting up libsepol2:amd64 (3.4-2.1) ... Selecting previously unselected package libsemanage2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49256 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1+b5_amd64.deb ... Unpacking libsemanage2:amd64 (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.4-1+b5) ... (Reading database ... (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 ... 49261 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-1+b1_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-1+b1) over (1:4.8.1-1) ... Setting up passwd (1:4.13+dfsg1-1+b1) ... Installing new version of config file /etc/default/useradd ... (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 ... 49296 files and directories currently installed.) Removing libsemanage1:amd64 (3.1-1+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49291 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Replacing files in old package libpam-modules:amd64 (1.4.0-9+deb11u1) ... Setting up libpam-modules-bin (1.5.2-6+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49298 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam-modules:amd64 (1.5.2-6+deb12u1) ... Installing new version of config file /etc/security/limits.conf ... Installing new version of config file /etc/security/sepermit.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49299 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.134_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.134) over (3.118+deb11u1) ... Setting up adduser (3.134) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49267 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-1.1_amd64.deb ... Unpacking gpgv (2.2.40-1.1) over (2.2.27-2+deb11u2) ... Setting up gpgv (2.2.40-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49267 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.3+deb12u1_all.deb ... Unpacking debian-archive-keyring (2023.3+deb12u1) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.3+deb12u1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49267 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1+b3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-1+b3) over (2.5.1-1+deb11u1) ... Setting up libseccomp2:amd64 (2.5.4-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49268 files and directories currently installed.) Preparing to unpack .../archives/apt_2.6.1_amd64.deb ... Unpacking apt (2.6.1) over (2.2.4) ... Setting up apt (2.6.1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49265 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.270_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.270) over (0.260) ... Setting up libdebconfclient0:amd64 (0.270) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49265 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.1_amd64.deb ... Unpacking base-passwd (3.6.1) over (3.5.51) ... Setting up base-passwd (3.6.1) ... Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 49265 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... 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Installing new version of config file /etc/init.d/x11-common ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libtry-tiny-perl (0.31-2) ... 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 perl-openssl-defaults:amd64 (7+b1) ... Setting up linux-libc-dev:amd64 (6.1.76-1) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libjemalloc2:amd64 (5.3.0-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libasan6:amd64 (11.3.0-12) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up tzdata (2024a-0+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Mar 27 23:35:04 UTC 2024. Universal Time is now: Wed Mar 27 23:35:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libjellyfish-2.0-2:amd64 (2.3.0-15+b3) ... Setting up libasound2-data (1.2.8-1) ... Setting up zip (3.0-13) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libblas3:amd64 (3.11.0-2) ... Setting up libuv1:amd64 (1.44.2-1) ... 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 libnspr4:amd64 (2:4.35-1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... 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 libatinject-jsr330-api-java (1.0+ds1-5) ... 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 libpng16-16:amd64 (1.6.39-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libio-html-perl (1.004-3) ... Setting up libss2:amd64 (1.47.0-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up util-linux (2.38.1-5+b1) ... 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 libbamtools2.5.2:amd64 (2.5.2+dfsg-4) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up logsave (1.47.0-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libvulkan1:amd64 (1.3.239.0-1) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up libprotobuf32:amd64 (3.21.12-3) ... Setting up mount (2.38.1-5+b1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up subread (2.0.3+dfsg-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 libxcb-randr0:amd64 (1.15-1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up netbase (6.4) ... Installing new version of config file /etc/ethertypes ... Installing new version of config file /etc/protocols ... Installing new version of config file /etc/rpc ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up mawk (1.3.4.20200120-3.1) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libc-dev-bin (2.36-9+deb12u4) ... Setting up openssl (3.0.11-1~deb12u2) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up liburi-perl (5.17-1) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up gmap (2021-12-17+ds-3) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libtsan0:amd64 (11.3.0-12) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... Setting up parafly (0.1.0-4) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up liblapack3:amd64 (3.11.0-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up fontconfig-config (2.14.1-4) ... Installing new version of config file /etc/fonts/conf.d/README ... Installing new version of config file /etc/fonts/fonts.conf ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libnet-http-perl (6.22-1) ... Setting up e2fsprogs (1.47.0-2) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libtbbbind-2-5:amd64 (2021.8.0-2) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 26 added, 15 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up shared-mime-info (2.2-1) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up berkeley-express (1.5.3+dfsg-3+b1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u5) ... Setting up libc6-dev:amd64 (2.36-9+deb12u4) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up curl (7.88.1-10+deb12u5) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up ca-certificates-java (20230710~deb12u1) ... Installing new version of config file /etc/ca-certificates/update.d/jks-keystore ... Removing debian:chambers_of_commerce_root_-_2008.pem Removing debian:cybertrust_global_root.pem Removing debian:dst_root_ca_x3.pem Removing debian:ec-acc.pem Removing debian:geotrust_primary_certification_authority_-_g2.pem Removing debian:global_chambersign_root_-_2008.pem Removing debian:globalsign_root_ca_-_r2.pem Removing debian:hellenic_academic_and_research_institutions_rootca_2011.pem Removing debian:network_solutions_certificate_authority.pem Removing debian:quovadis_root_ca.pem Removing debian:sonera_class_2_root_ca.pem Removing debian:staat_der_nederlanden_ev_root_ca.pem Removing debian:staat_der_nederlanden_root_ca_-_g3.pem Removing debian:trustis_fps_root_ca.pem Removing debian:verisign_universal_root_certification_authority.pem Replacing debian:ACCVRAIZ1.pem Replacing debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Replacing debian:Actalis_Authentication_Root_CA.pem Replacing debian:AffirmTrust_Commercial.pem Replacing debian:AffirmTrust_Networking.pem Replacing debian:AffirmTrust_Premium.pem Replacing debian:AffirmTrust_Premium_ECC.pem Replacing debian:Amazon_Root_CA_1.pem Replacing debian:Amazon_Root_CA_2.pem Replacing debian:Amazon_Root_CA_3.pem Replacing debian:Amazon_Root_CA_4.pem Replacing debian:Atos_TrustedRoot_2011.pem Replacing debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Replacing debian:Baltimore_CyberTrust_Root.pem Replacing debian:Buypass_Class_2_Root_CA.pem Replacing debian:Buypass_Class_3_Root_CA.pem Replacing debian:CA_Disig_Root_R2.pem Replacing debian:CFCA_EV_ROOT.pem Replacing debian:COMODO_Certification_Authority.pem Replacing debian:COMODO_ECC_Certification_Authority.pem Replacing debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Replacing debian:Certigna.pem Replacing debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Replacing debian:Certum_Trusted_Network_CA.pem Replacing debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Replacing 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 Replacing debian:D-TRUST_Root_Class_3_CA_2_2009.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Replacing debian:DigiCert_Assured_ID_Root_CA.pem Replacing debian:DigiCert_Assured_ID_Root_G2.pem Replacing debian:DigiCert_Assured_ID_Root_G3.pem Replacing debian:DigiCert_Global_Root_CA.pem Replacing debian:DigiCert_Global_Root_G2.pem Replacing debian:DigiCert_Global_Root_G3.pem Replacing 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 Replacing debian:DigiCert_Trusted_Root_G4.pem Replacing 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 Replacing debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Replacing debian:Entrust_Root_Certification_Authority.pem Replacing debian:Entrust_Root_Certification_Authority_-_EC1.pem Replacing debian:Entrust_Root_Certification_Authority_-_G2.pem Replacing debian:Entrust_Root_Certification_Authority_-_G4.pem Replacing debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Replacing debian:GTS_Root_R1.pem Replacing debian:GTS_Root_R2.pem Replacing debian:GTS_Root_R3.pem Replacing debian:GTS_Root_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R5.pem Replacing debian:GlobalSign_Root_CA.pem Replacing debian:GlobalSign_Root_CA_-_R3.pem Replacing debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Replacing debian:Go_Daddy_Class_2_CA.pem Replacing 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 Replacing debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Replacing debian:Hongkong_Post_Root_CA_1.pem Replacing debian:Hongkong_Post_Root_CA_3.pem Replacing debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Replacing debian:IdenTrust_Commercial_Root_CA_1.pem Replacing debian:IdenTrust_Public_Sector_Root_CA_1.pem Replacing debian:Izenpe.com.pem Replacing debian:Microsec_e-Szigno_Root_CA_2009.pem Replacing debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Replacing debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Replacing debian:NAVER_Global_Root_Certification_Authority.pem Replacing debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Replacing debian:OISTE_WISeKey_Global_Root_GB_CA.pem Replacing debian:OISTE_WISeKey_Global_Root_GC_CA.pem Replacing debian:QuoVadis_Root_CA_1_G3.pem Replacing debian:QuoVadis_Root_CA_2.pem Replacing debian:QuoVadis_Root_CA_2_G3.pem Replacing debian:QuoVadis_Root_CA_3.pem Replacing debian:QuoVadis_Root_CA_3_G3.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Replacing debian:SSL.com_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_Root_Certification_Authority_RSA.pem Replacing debian:SZAFIR_ROOT_CA2.pem Replacing debian:SecureSign_RootCA11.pem Replacing debian:SecureTrust_CA.pem Replacing debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Replacing debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Replacing debian:Security_Communication_Root_CA.pem Replacing debian:Starfield_Class_2_CA.pem Replacing debian:Starfield_Root_Certificate_Authority_-_G2.pem Replacing debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Replacing debian:SwissSign_Gold_CA_-_G2.pem Replacing debian:SwissSign_Silver_CA_-_G2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_3.pem Replacing debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Replacing debian:TWCA_Global_Root_CA.pem Replacing debian:TWCA_Root_Certification_Authority.pem Replacing debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Replacing debian:TrustCor_ECA-1.pem Replacing debian:TrustCor_RootCert_CA-1.pem Replacing debian:TrustCor_RootCert_CA-2.pem Replacing debian:Trustwave_Global_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Replacing debian:UCA_Extended_Validation_Root.pem Replacing debian:UCA_Global_G2_Root.pem Replacing debian:USERTrust_ECC_Certification_Authority.pem Replacing debian:USERTrust_RSA_Certification_Authority.pem Replacing debian:XRamp_Global_CA_Root.pem Replacing debian:certSIGN_ROOT_CA.pem Replacing debian:certSIGN_Root_CA_G2.pem Replacing debian:e-Szigno_Root_CA_2017.pem Replacing debian:ePKI_Root_Certification_Authority.pem Replacing debian:emSign_ECC_Root_CA_-_C3.pem Replacing debian:emSign_ECC_Root_CA_-_G3.pem Replacing debian:emSign_Root_CA_-_C1.pem Replacing debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... 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 libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Setting up libtbb12:amd64 (2021.8.0-2) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... 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 libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libstaden-read14:amd64 (1.14.15-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libwww-perl (6.68-1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up python3 (3.11.2-1+b1) ... Setting up rna-star (2.7.10b+dfsg-2+b2) ... Setting up samtools (1.16.1-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up salmon (1.10.1+ds1-1+b1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up jellyfish (2.3.0-15+b3) ... Setting up r-base-core (4.2.2.20221110-2) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/Renviron.site ... Installing new version of config file /etc/R/repositories ... Replacing config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up r-cran-biasedurn (2.0.9-1) ... 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 (17.0.10+7-1~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-xml (3.99-0.13-1) ... Setting up hisat2 (2.2.1-4+b2) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up r-cran-locfit (1.5-9.7-1) ... Setting up r-cran-cluster (2.1.4-1) ... Setting up rsem (1.3.3+dfsg-2+b1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-clipr (0.8.0-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up r-cran-fastcluster (1.2.3-2) ... Setting up kallisto (0.48.0+dfsg-3) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-filelock (1.0.2-2) ... Setting up r-bioc-genomeinfodbdata (1.2.9-1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up transdecoder (5.0.1-5) ... 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-openssl (2.0.5+dfsg-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-cran-brio (1.1.3-1+b1) ... Setting up r-cran-diffobj (0.3.5-1+b1) ... 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 python3-pysam (0.20.0+ds-3+b1) ... Setting up littler (0.3.17-1) ... Setting up python3-hisat2 (2.2.1-4) ... Setting up bowtie (1.3.1-1+b1) ... Setting up r-cran-amap (0.8-19-1) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... Setting up r-cran-sys (3.4.1-1) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-processx (3.8.0-1) ... Setting up r-cran-mime (0.12-1+b1) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-digest (0.6.31-1) ... Setting up r-cran-ape (5.7-1) ... Setting up r-cran-yaml (2.3.7-1) ... Setting up r-cran-xml2 (1.3.3-1+b1) ... Setting up r-cran-evaluate (0.20-1) ... Setting up r-cran-dbi (1.1.3-1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-gtools (3.9.4-1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-bit (4.0.5-1) ... 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 r-cran-rprojroot (2.0.3-1) ... Setting up r-bioc-zlibbioc (1.44.0+dfsg-1) ... Setting up r-cran-fastmap (1.1.1-1) ... Setting up r-cran-png (0.1-8-1) ... Setting up r-bioc-biobase (2.58.0-2) ... Setting up r-cran-jsonlite (1.8.4+dfsg-1) ... Setting up r-cran-rstudioapi (0.14-1) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-stringi (1.7.12-1) ... Setting up r-cran-hwriter (1.3.2.1-1) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up r-bioc-rots (1.26.0-1) ... Setting up r-cran-cpp11 (0.4.3-1) ... Setting up r-cran-plyr (1.8.8-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-bioc-limma (3.54.1+dfsg-1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up r-bioc-tximport (1.26.1+dfsg-1) ... Setting up r-cran-kernsmooth (2.23-20-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up r-cran-cachem (1.0.7-1) ... Setting up r-cran-catools (1.18.2-1+b1) ... Setting up r-cran-rcpparmadillo (0.12.0.1.0-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up r-bioc-ctc (1.72.0-1) ... Setting up r-cran-rjson (0.2.21-1) ... Setting up r-cran-tzdb (0.3.0-1) ... Setting up r-cran-argparse (2.2.2+dfsg-1) ... Setting up r-cran-rcurl (1.98-1.10+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up python3-htseq (1.99.2-1+b3) ... Setting up r-cran-gdata (2.18.0.1-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-stringr (1.5.0-1) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up r-cran-callr (3.7.3-2) ... Setting up r-bioc-edger (3.40.2+dfsg-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-cran-desc (1.4.2-1) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up r-cran-survival (3.5-3-1) ... Setting up r-bioc-biocio (1.8.0+dfsg-1) ... Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-waldo (0.4.0-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-blob (1.2.3-1) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up r-cran-pkgbuild (1.4.0-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up r-cran-dbplyr (2.3.0+dfsg-1) ... Setting up r-cran-gplots (3.1.3-1) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-pkgload (1.3.2-1) ... Setting up r-cran-vroom (1.6.1-1) ... Setting up r-bioc-biocfilecache (2.6.1+dfsg-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-cran-testthat (3.1.6-1) ... Setting up r-cran-readr (2.1.4-1) ... Setting up r-cran-ggdendro (0.1.23+dfsg-1) ... Setting up r-bioc-rsamtools (2.14.0-1) ... Setting up r-bioc-qvalue (2.30.0-1) ... Setting up r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Setting up r-bioc-keggrest (1.38.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.60.0-1) ... Setting up r-bioc-go.db (3.16.0-1) ... Setting up r-bioc-annotate (1.76.0+dfsg-1) ... Setting up r-bioc-biomart (2.54.0+dfsg-1) ... Setting up r-bioc-genefilter (1.80.3-1) ... Setting up r-bioc-genomicalignments (1.34.0-1) ... Setting up r-bioc-geneplotter (1.76.0-1) ... Setting up r-bioc-rtracklayer (1.58.0-1) ... Setting up r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Setting up r-bioc-deseq2 (1.38.3+dfsg-1) ... Setting up r-bioc-dexseq (1.44.0+dfsg-1) ... Setting up r-bioc-genelendatabase (1.34.0-1) ... Setting up r-bioc-goseq (1.50.0-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (31.1-1) ... Setting up libjung-free-java (2.1.1-2) ... Processing triggers for debianutils (5.7-0.5~deb12u1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... Processing triggers for ca-certificates-java (20230710~deb12u1) ... done. Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre:amd64 (17.0.10+7-1~deb12u1) ... Setting up jaligner (1.0+dfsg-10) ... Setting up default-jre (2:1.17-74) ... 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. 3m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 3m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m57.4s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 3m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 3m57.6s DUMP: Package: trinityrnaseq Status: install ok installed Priority: optional Section: science Installed-Size: 7229 Maintainer: Debian Med Packaging Team Architecture: amd64 Version: 2.11.0+dfsg-6 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl, salmon, python3-numpy, ncbi-blast+, python3, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-fastcluster, liburi-perl, r-cran-ape, r-bioc-ctc, r-cran-gplots, r-bioc-biobase, r-bioc-goseq, r-bioc-tximport, python3-htseq, rna-star, gmap, hisat2, subread, kallisto, python3-hisat2, r-cran-argparse, r-cran-goplot, r-bioc-dexseq Recommends: trinityrnaseq-examples, r-cran-tidyverse, picard-tools, tabix Suggests: collectl, r-bioc-tximportdata Description: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: https://trinityrnaseq.github.io/ 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 3m57.6s INFO: apt-cache does not know about any of the requested packages 3m57.6s INFO: Running scripts post_distupgrade 3m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_exceptions'] 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_exceptions'] 3m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_zz_backports'] 3m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_zz_backports'] 3m57.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 3m59.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 3m59.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpizzr_c2w to sid 3m59.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 3m59.5s INFO: Running scripts pre_distupgrade 3m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 3m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 3m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_exceptions'] 3m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_exceptions'] 3m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 3m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 3m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 3m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_database-server'] 3m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 3m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 3m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 4m3.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9941 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7210 kB] Fetched 17.3 MB in 3s (5571 kB/s) Reading package lists... 4m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'update'] 4m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 5m47.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fonts-font-awesome fonts-lato gcc-11-base gcc-12-base libapache-pom-java libasan6 libbamtools2.5.1 libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libgcc-10-dev libgcc-12-dev libglib2.0-0 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnsl-dev libperl5.32 libperl5.36 libprotobuf23 libpython3.9-minimal libpython3.9-stdlib libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libvecmath-java libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis sphinx-rtd-theme-common Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libasound2 libatk1.0-0 libboost1.74-dev libcups2 libcurl3-gnutls libcurl4 libdb5.3 libelf1 libext2fs2 libgdbm-compat4 libgdbm6 libgnutls30 libgtk2.0-0 libhogweed6 libhts3 libmbedcrypto7 libmbedtls14 libmbedx509-1 libnettle8 libpng16-16 libprotobuf32 libpsl5 libreadline8 libssh2-1 libssl3 libstaden-read14 libtirpc3 libuv1 libxt6 The following NEW packages will be installed: fonts-dejavu-mono gcc-13-base gcc-14-base libapt-pkg6.0t64 libasound2t64 libatk1.0-0t64 libboost-filesystem1.83.0 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libboost1.83-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libelf1t64 libext2fs2t64 libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libgtk2.0-0t64 libhogweed6t64 libhts3t64 libhwasan0 libllvm17t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libnettle8t64 libperl5.38t64 libpng16-16t64 libprotobuf32t64 libpsl5t64 libreadline8t64 libsharpyuv0 libssh2-1t64 libssl3t64 libstaden-read14t64 libstdc++-13-dev libtirpc3t64 libunistring5 libuv1t64 libxt6t64 perl-modules-5.38 r-bioc-s4arrays r-bioc-sparsearray r-cran-abind r-cran-tidyr The following packages will be upgraded: adduser adwaita-icon-theme apt at-spi2-common base-files base-passwd bash berkeley-express bowtie bowtie2 bsdutils ca-certificates ca-certificates-java coreutils curl dash debconf debian-archive-keyring debianutils default-jre default-jre-headless diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core fonts-lato gcc-10-base gcc-11-base gcc-12-base gcc-9-base gmap gpgv grep gtk-update-icon-cache gzip hisat2 hostname init-system-helpers jaligner java-common jellyfish kallisto libacl1 libasan6 libasan8 libasound2-data libatomic1 libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libblas3 libblkid1 libboost-dev libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libclone-perl libcolt-free-java libcom-err2 libcommons-collections4-java libcrypt-dev libcrypt1 libdatrie1 libdbus-1-3 libdebconfclient0 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libexpat1 libffi8 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-s1 libgcrypt20 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libgtk2.0-common libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhwloc15 libicu72 libidn2-0 libio-socket-ssl-perl libitm1 libjbig0 libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-sphinxdoc libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblmdb0 liblsan0 liblwp-protocol-https-perl liblz4-1 liblzma5 libmd0 libmount1 libmpdec3 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl-dev libnsl2 libnspr4 libnss3 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-8-0 libpcre3 libpcsclite1 libpixman-1-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsensors-config libsensors5 libsepol2 libsmartcols1 libsqlite3-0 libss2 libstdc++-10-dev libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan0 libtsan2 libubsan1 libudev1 liburi-perl libuuid1 libvulkan1 libwebp7 libwww-perl libx11-6 libx11-data libx11-xcb1 libxft2 libxi6 libxml2 libxrandr2 libxxhash0 libz3-4 libzstd1 linux-libc-dev littler login logsave mawk media-types mount ncbi-blast+ ncbi-data ncurses-base ncurses-bin openjdk-11-jre openjdk-11-jre-headless openjdk-17-jre openjdk-17-jre-headless openssl passwd perl perl-base perl-openssl-defaults python3 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.11 python3.11-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-ctc r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-ape r-cran-askpass r-cran-bh r-cran-biasedurn r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-cluster r-cran-cpp11 r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastcluster r-cran-filelock r-cran-findpython r-cran-fs r-cran-gdata r-cran-ggplot2 r-cran-glue r-cran-gplots r-cran-gtable r-cran-gtools r-cran-hms r-cran-httr r-cran-jsonlite r-cran-kernsmooth r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-png r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-testthat r-cran-tibble r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rna-star rsem salmon samtools sed sensible-utils shared-mime-info sphinx-rtd-theme-common subread sysvinit-utils tar transdecoder trinityrnaseq tzdata usrmerge util-linux util-linux-extra zlib1g zlib1g-dev 394 upgraded, 50 newly installed, 30 to remove and 0 not upgraded. Need to get 687 MB of archives. After this operation, 486 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-11 [97.4 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3+b1 [67.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.2 [10.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.2 [189 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:12 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:13 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:14 http://deb.debian.org/debian sid/main amd64 curl amd64 8.6.0-4 [341 kB] Get:15 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1+b1 [787 kB] Get:16 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.0+dfsg-1+b1 [176 kB] Get:17 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.62.0-1 [2119 kB] Get:18 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2062 kB] Get:19 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.36.0-1 [2258 kB] Get:20 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.2-1 [824 kB] Get:21 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240315-1 [42.9 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240315-1 [72.2 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240315-1 [713 kB] Get:24 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:25 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:26 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:27 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:28 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:29 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:30 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get:31 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.4-1 [1159 kB] Get:32 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:33 http://deb.debian.org/debian sid/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:34 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:35 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:36 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3+b2 [597 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3+b2 [1879 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3+b2 [1792 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3+b2 [817 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:43 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:47 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.1.1+dfsg-2+b1 [397 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-6 [275 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-6 [1222 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libatk1.0-0t64 amd64 2.51.90-4 [50.7 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1+b1 [1426 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.6.0-4 [421 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b1 [266 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.6.0-4 [430 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get:75 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4266 kB] Get:79 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2 [236 kB] Get:80 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2 [1643 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:84 http://deb.debian.org/debian sid/main amd64 liburi-perl all 5.27-1 [98.4 kB] Get:85 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:86 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:88 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:93 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b1 [75.0 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:110 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-11 [160 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-11 [191 kB] Get:112 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.51.90-4 [165 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get:114 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:115 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:116 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:117 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:118 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-11 [117 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-11 [30.2 kB] Get:124 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-11 [155 kB] Get:125 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-11 [1231 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get:127 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre amd64 17.0.11~7ea-1 [185 kB] Get:128 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.11~7ea-1 [43.8 MB] Get:129 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:134 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libelf1t64 amd64 0.191-1 [189 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libllvm17t64 amd64 1:17.0.6-9 [23.7 MB] Get:148 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.3.275.0-1 [124 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.0.3-1+b1 [8281 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.0.3-1+b1 [151 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.0.3-1+b1 [36.5 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b2 [438 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:161 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:162 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:163 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:167 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre amd64 11.0.23~7ea-1 [194 kB] Get:168 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.23~7ea-1 [38.3 MB] Get:169 http://deb.debian.org/debian sid/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:172 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-3 [758 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:177 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b2 [138 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-3 [278 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3 [530 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:186 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:191 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get:192 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1+b1 [74.1 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:197 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get:198 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get:199 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:200 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get:201 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.42.0-1 [622 kB] Get:202 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB] Get:203 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3848 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.70.3+dfsg-1 [13.7 MB] Get:205 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB] Get:206 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.64.1-1 [4705 kB] Get:207 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.16.1-1 [1751 kB] Get:208 http://deb.debian.org/debian sid/main amd64 r-bioc-annotate all 1.80.0+dfsg-1 [1739 kB] Get:209 http://deb.debian.org/debian sid/main amd64 r-bioc-tximport all 1.30.0+dfsg-1 [89.9 kB] Get:210 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240315-1 [836 kB] Get:213 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:214 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:215 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:216 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [504 kB] Get:217 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.2.0-1 [484 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get:219 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1196 kB] Get:220 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1794 kB] Get:221 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1827 kB] Get:222 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1139 kB] Get:223 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-21 [44.3 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240315-1 [136 kB] Get:225 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240315-1 [25.8 kB] Get:226 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240315-1 [9224 B] Get:227 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240315-1 [2724 kB] Get:228 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240315-1 [1201 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240315-1 [1071 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.3.0-15 [2069 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240315-1 [147 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.3.0-15 [2435 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240315-1 [2454 kB] Get:234 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-15 [41.8 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240315-1 [1485 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-21 [2537 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-21 [2264 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:239 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get:240 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:241 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.36.0-1 [1337 kB] Get:242 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2144 kB] Get:243 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.12.0+dfsg-1 [214 kB] Get:244 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5094 kB] Get:245 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:246 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-1 [16.0 kB] Get:247 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:248 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get:249 http://deb.debian.org/debian sid/main amd64 r-bioc-rots amd64 1.30.0-1 [419 kB] Get:250 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3 [1285 kB] Get:251 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get:252 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:253 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:254 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:255 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:256 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:257 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:258 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:259 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:260 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:261 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:262 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:263 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get:264 http://deb.debian.org/debian sid/main amd64 r-bioc-qvalue all 2.34.0-1 [2805 kB] Get:265 http://deb.debian.org/debian sid/main amd64 r-bioc-limma amd64 3.58.1+dfsg-1 [1951 kB] Get:266 http://deb.debian.org/debian sid/main amd64 r-cran-biasedurn amd64 2.0.11-1 [277 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:270 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.3-1 [861 kB] Get:271 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:272 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.35-1 [203 kB] Get:273 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:274 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:275 http://deb.debian.org/debian sid/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:276 http://deb.debian.org/debian sid/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get:277 http://deb.debian.org/debian sid/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:278 http://deb.debian.org/debian sid/main amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [301 kB] Get:279 http://deb.debian.org/debian sid/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get:280 http://deb.debian.org/debian sid/main amd64 r-bioc-biomart all 2.58.2+dfsg-1 [450 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.54.3+dfsg-1 [1665 kB] Get:282 http://deb.debian.org/debian sid/main amd64 r-bioc-genelendatabase all 1.38.0-1 [100 MB] Get:283 http://deb.debian.org/debian sid/main amd64 r-bioc-go.db all 3.18.0-1 [12.1 MB] Get:284 http://deb.debian.org/debian sid/main amd64 r-bioc-goseq all 1.54.0-1 [1720 kB] Get:285 http://deb.debian.org/debian sid/main amd64 r-bioc-geneplotter all 1.80.0+dfsg-1 [1416 kB] Get:286 http://deb.debian.org/debian sid/main amd64 r-cran-survival amd64 3.5-8-1 [6149 kB] Get:287 http://deb.debian.org/debian sid/main amd64 r-bioc-genefilter amd64 1.84.0-1 [1115 kB] Get:288 http://deb.debian.org/debian sid/main amd64 r-cran-locfit amd64 1.5-9.8-1 [508 kB] Get:289 http://deb.debian.org/debian sid/main amd64 r-bioc-edger amd64 4.0.16+dfsg-1 [1149 kB] Get:290 http://deb.debian.org/debian sid/main amd64 r-cran-rcpparmadillo amd64 0.12.8.1.0-1 [879 kB] Get:291 http://deb.debian.org/debian sid/main amd64 r-bioc-deseq2 amd64 1.42.1+dfsg-1 [1267 kB] Get:292 http://deb.debian.org/debian sid/main amd64 r-bioc-dexseq all 1.48.0+dfsg-1 [466 kB] Get:293 http://deb.debian.org/debian sid/main amd64 r-bioc-ctc all 1.76.0-1 [138 kB] Get:294 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1+b1 [3584 kB] Get:295 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:296 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:297 http://deb.debian.org/debian sid/main amd64 r-cran-ps amd64 1.7.6-1 [310 kB] Get:298 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:299 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:300 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:301 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-3+b1 [26.8 MB] Get:302 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.2 [82.6 kB] Get:303 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b1 [40.4 kB] Get:304 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.7.9-2 [2255 kB] Get:305 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:306 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:307 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:308 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:309 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:310 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:311 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.14 [986 kB] Get:312 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.14 [1370 kB] Get:313 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:314 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:315 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:316 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:317 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:318 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:319 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:320 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:321 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:322 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:323 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:324 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b3 [10.2 kB] Get:325 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:326 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:327 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:328 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b3 [90.3 kB] Get:329 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:330 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:331 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-3 [649 kB] Get:332 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:333 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:334 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:335 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:336 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:337 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:338 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:339 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:340 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get:341 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:342 http://deb.debian.org/debian sid/main amd64 libmbedtls14t64 amd64 2.28.7-1.1 [166 kB] Get:343 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7t64 amd64 2.28.7-1.1 [280 kB] Get:344 http://deb.debian.org/debian sid/main amd64 libmbedx509-1t64 amd64 2.28.7-1.1 [130 kB] Get:345 http://deb.debian.org/debian sid/main amd64 berkeley-express amd64 1.5.3+dfsg-3+b3 [233 kB] Get:346 http://deb.debian.org/debian sid/main amd64 libprotobuf32t64 amd64 3.21.12-8.2 [963 kB] Get:347 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.3+dfsg-1+b1 [228 kB] Get:348 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get:349 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-11 [143 kB] Get:350 http://deb.debian.org/debian sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:351 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:352 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:353 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:354 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:355 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:356 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:357 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:358 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:359 http://deb.debian.org/debian sid/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [159 kB] Get:360 http://deb.debian.org/debian sid/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-2.1+b1 [280 kB] Get:361 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1+b1 [345 kB] Get:362 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libboost-program-options1.74.0 amd64 1.74.0+ds1-23.1+b1 [332 kB] Get:384 http://deb.debian.org/debian sid/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-23.1+b1 [256 kB] Get:385 http://deb.debian.org/debian sid/main amd64 libcolt-free-java all 1.2.0+dfsg-8 [440 kB] Get:386 http://deb.debian.org/debian sid/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get:387 http://deb.debian.org/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:388 http://deb.debian.org/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:389 http://deb.debian.org/debian sid/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:390 http://deb.debian.org/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:391 http://deb.debian.org/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:392 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get:393 http://deb.debian.org/debian sid/main amd64 libio-socket-ssl-perl all 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http://deb.debian.org/debian sid/main amd64 rna-star amd64 2.7.11b+dfsg-1+b1 [3444 kB] Get:439 http://deb.debian.org/debian sid/main amd64 rsem amd64 1.3.3+dfsg-3+b1 [36.1 MB] Get:440 http://deb.debian.org/debian sid/main amd64 salmon amd64 1.10.2+ds1-1+b2 [3268 kB] Get:441 http://deb.debian.org/debian sid/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get:442 http://deb.debian.org/debian sid/main amd64 subread amd64 2.0.6+dfsg-2 [826 kB] Get:443 http://deb.debian.org/debian sid/main amd64 transdecoder all 5.7.1-2 [205 kB] Get:444 http://deb.debian.org/debian sid/main amd64 trinityrnaseq amd64 2.15.1+dfsg-5+b1 [1720 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 687 MB in 12s (56.3 MB/s) (Reading database ... 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Unpacking libpython3.11-minimal:amd64 (3.11.8-3+b2) over (3.11.2-6) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libreadline8 (>= 6.0). libpython3.9-stdlib:amd64 depends on libreadline8 (>= 7.0~beta). (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 ... 59921 files and directories currently installed.) Removing libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libreadline8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59908 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) over (8.2-1.3) ... Preparing to unpack .../libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) over (6.4-4) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.4-4) ... 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Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2+b1) over (2:6.2.1+dfsg1-1.1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59933 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.5+dfsg2-2_amd64.deb ... Unpacking libzstd1:amd64 (1.5.5+dfsg2-2) over (1.5.4+dfsg2-5) ... Setting up libzstd1:amd64 (1.5.5+dfsg2-2) ... (Reading database ... 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Installing new version of config file /etc/security/namespace.init ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. libpython3.9-stdlib:amd64 depends on libdb5.3. libperl5.36:amd64 depends on libdb5.3. libperl5.32:amd64 depends on libdb5.3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59930 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59924 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59920 files and directories currently installed.) Preparing to unpack .../libcups2t64_2.4.7-1.2+b1_amd64.deb ... Unpacking libcups2t64:amd64 (2.4.7-1.2+b1) ... Preparing to unpack .../libglib2.0-0_2.78.4-6_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.78.4-6) over (2.74.6-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../libglib2.0-0t64_2.78.4-6_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.78.4-6) ... dpkg: libatk1.0-0:amd64: dependency problems, but removing anyway as you requested: libgtk2.0-0:amd64 depends on libatk1.0-0 (>= 1.32.0). (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 ... 59934 files and directories currently installed.) Removing libatk1.0-0:amd64 (2.46.0-5) ... Selecting previously unselected package libatk1.0-0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59928 files and directories currently installed.) Preparing to unpack .../libatk1.0-0t64_2.51.90-4_amd64.deb ... Unpacking libatk1.0-0t64:amd64 (2.51.90-4) ... dpkg: libgtk2.0-0:amd64: dependency problems, but removing anyway as you requested: openjdk-17-jre:amd64 depends on libgtk2.0-0 | libgtk-3-0; however: Package libgtk2.0-0:amd64 is to be removed. Package libgtk-3-0 is not installed. (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 ... 59934 files and directories currently installed.) Removing libgtk2.0-0:amd64 (2.24.33-2) ... Selecting previously unselected package libgtk2.0-0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59902 files and directories currently installed.) Preparing to unpack .../libgtk2.0-0t64_2.24.33-4_amd64.deb ... libgtk2.0-0t64.preinst: Removing /var/lib/dpkg/info/libgtk2.0-0:amd64.postrm to avoid loss of /usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/immodules.cache... removed '/var/lib/dpkg/info/libgtk2.0-0:amd64.postrm' Unpacking libgtk2.0-0t64:amd64 (2.24.33-4) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59934 files and directories currently installed.) Removing libhogweed6:amd64 (3.8.1-2) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libnettle8 (>= 3.7~). libcurl3-gnutls:amd64 depends on libnettle8. Removing libnettle8:amd64 (3.8.1-2) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: libldap-2.4-2:amd64 depends on libgnutls30 (>= 3.7.0). libcurl3-gnutls:amd64 depends on libgnutls30 (>= 3.7.5). apt depends on libgnutls30 (>= 3.7.5). Removing libgnutls30:amd64 (3.7.9-2+deb12u2) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59891 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... Selecting previously unselected package libhogweed6t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59900 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59907 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59907 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1+b1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1+b1) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1+b1) ... dpkg: libssh2-1:amd64: dependency problems, but removing anyway as you requested: libcurl4:amd64 depends on libssh2-1 (>= 1.7.0). libcurl3-gnutls:amd64 depends on libssh2-1 (>= 1.7.0). (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 ... 59937 files and directories currently installed.) Removing libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libssh2-1t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59928 files and directories currently installed.) Preparing to unpack .../libssh2-1t64_1.11.0-4.1+b1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b1) ... dpkg: libcurl3-gnutls:amd64: dependency problems, but removing anyway as you requested: libstaden-read14:amd64 depends on libcurl3-gnutls (>= 7.16.2). libhts3:amd64 depends on libcurl3-gnutls (>= 7.18.0). (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 ... 59938 files and directories currently installed.) Removing libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59930 files and directories currently installed.) Preparing to unpack .../libcurl3t64-gnutls_8.6.0-4_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.6.0-4) ... dpkg: libstaden-read14:amd64: dependency problems, but removing anyway as you requested: salmon depends on libstaden-read14 (>= 1.14.12). (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59940 files and directories currently installed.) Removing libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package libpsl5t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59934 files and directories currently installed.) Preparing to unpack .../libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... dpkg: libcurl4:amd64: dependency problems, but removing anyway as you requested: r-bioc-rsamtools depends on libcurl4 (>= 7.18.0). r-bioc-rhtslib depends on libcurl4 (>= 7.18.0). r-base-core depends on libcurl4 (>= 7.28.0). (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 ... 59941 files and directories currently installed.) Removing libcurl4:amd64 (7.88.1-10+deb12u5) ... Selecting previously unselected package libcurl4t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59935 files and directories currently installed.) Preparing to unpack .../libcurl4t64_8.6.0-4_amd64.deb ... Unpacking libcurl4t64:amd64 (8.6.0-4) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libnet-ssleay-perl:amd64 depends on libssl3 (>= 3.0.0). libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). libhts3:amd64 depends on libssl3 (>= 3.0.0). (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 ... 59942 files and directories currently installed.) Removing libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libssl3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59930 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.1.5-1.1_amd64.deb ... Unpacking libssl3t64:amd64 (3.1.5-1.1) ... Setting up libssl3t64:amd64 (3.1.5-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59945 files and directories currently installed.) Preparing to unpack .../libnet-ssleay-perl_1.94-1+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.94-1+b1) over (1.92-2+b1) ... Preparing to unpack .../libhtml-parser-perl_3.82-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.82-1) over (3.81-1) ... Preparing to unpack .../libclone-perl_0.46-1+b2_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1+b2) over (0.46-1) ... Preparing to unpack .../perl_5.38.2-3.2_amd64.deb ... Unpacking perl (5.38.2-3.2) over (5.36.0-7+deb12u1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested: libperl5.36:amd64 depends on libgdbm6 (>= 1.21). libperl5.32:amd64 depends on libgdbm6 (>= 1.18-3). libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16). (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 ... 61359 files and directories currently installed.) Removing libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm6t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61353 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1+b1) ... dpkg: libgdbm-compat4:amd64: dependency problems, but removing anyway as you requested: libperl5.36:amd64 depends on libgdbm-compat4 (>= 1.18-3). libperl5.32:amd64 depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61361 files and directories currently installed.) Removing libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61355 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../libperl5.38t64_5.38.2-3.2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2) ... Preparing to unpack .../perl-base_5.38.2-3.2_amd64.deb ... Unpacking perl-base (5.38.2-3.2) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-3.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61886 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-5+b1) ... Setting up libbz2-1.0:amd64 (1.0.8-5.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61885 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61885 files and directories currently installed.) Preparing to unpack .../libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) over (3.20-6) ... Preparing to unpack .../liburi-perl_5.27-1_all.deb ... Unpacking liburi-perl (5.27-1) over (5.17-1) ... Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.82) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61891 files and directories currently installed.) Preparing to unpack .../tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) over (2024a-0+deb12u1) ... Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61108 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.45.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.2-1) over (3.40.1-2) ... Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) over (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61108 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.47-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.47-3) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.47-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61108 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61108 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-1+b2_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1+b2) over (1.9.4-1) ... Setting up liblz4-1:amd64 (1.9.4-1+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61109 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60767 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271+b3_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271+b3) over (0.270) ... Setting up libdebconfclient0:amd64 (0.271+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60768 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60768 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60768 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.5-2) ... (Reading database ... (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 ... 60768 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b3_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b3) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.5-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60768 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-4) over (1:4.13+dfsg1-1+b1) ... Setting up passwd (1:4.13+dfsg1-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60767 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) over (3.134) ... Setting up adduser (3.137) ... Installing new version of config file /etc/adduser.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60761 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-3_amd64.deb ... Unpacking gpgv (2.2.40-3) over (2.2.40-1.1) ... Setting up gpgv (2.2.40-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60761 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.4_all.deb ... Unpacking debian-archive-keyring (2023.4) over (2023.3+deb12u1) ... Setting up debian-archive-keyring (2023.4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60761 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1) over (2.5.4-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60760 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.65.2) ... Setting up init-system-helpers (1.66) ... (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 ... 60760 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-base (6.4+20240113-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60758 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_amd64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60758 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4_amd64.deb ... Unpacking logsave (1.47.0-2.4) over (1.47.0-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60758 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2) ... Selecting previously unselected package libext2fs2t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60751 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.0-2.4) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up libext2fs2t64:amd64 (1.47.0-2.4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60767 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4_amd64.deb ... Unpacking e2fsprogs (1.47.0-2.4) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty dpkg: libhts3:amd64: dependency problems, but removing anyway as you requested: trinityrnaseq depends on libhts3 (>= 1.10). samtools depends on libhts3 (>= 1.16). rsem depends on libhts3 (>= 1.10). rna-star depends on libhts3 (>= 1.10). python3-pysam depends on libhts3 (>= 1.16). kallisto depends on libhts3 (>= 1.10). jellyfish depends on libhts3 (>= 1.10). (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 ... 60765 files and directories currently installed.) Removing libhts3:amd64 (1.16+ds-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60750 files and directories currently installed.) Preparing to unpack .../samtools_1.19.2-1+b1_amd64.deb ... Unpacking samtools (1.19.2-1+b1) over (1.16.1-1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../libhts3t64_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts3t64:amd64 (1.19+ds-1.1+b1) ... dpkg: libmbedtls14:amd64: dependency problems, but removing anyway as you requested: ncbi-blast+ depends on libmbedtls14 (>= 2.28.0). (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 ... 60770 files and directories currently installed.) Removing libmbedtls14:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedtls14t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60764 files and directories currently installed.) Preparing to unpack .../libmbedtls14t64_2.28.7-1.1_amd64.deb ... Unpacking libmbedtls14t64:amd64 (2.28.7-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60771 files and directories currently installed.) Removing libmbedx509-1:amd64 (2.28.3-1) ... dpkg: libmbedcrypto7:amd64: dependency problems, but removing anyway as you requested: ncbi-blast+ depends on libmbedcrypto7 (>= 2.28.0). Removing libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedcrypto7t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60759 files and directories currently installed.) Preparing to unpack .../libmbedcrypto7t64_2.28.7-1.1_amd64.deb ... Unpacking libmbedcrypto7t64:amd64 (2.28.7-1.1) ... Selecting previously unselected package libmbedx509-1t64:amd64. Preparing to unpack .../libmbedx509-1t64_2.28.7-1.1_amd64.deb ... Unpacking libmbedx509-1t64:amd64 (2.28.7-1.1) ... Preparing to unpack .../berkeley-express_1.5.3+dfsg-3+b3_amd64.deb ... Unpacking berkeley-express (1.5.3+dfsg-3+b3) over (1.5.3+dfsg-3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60773 files and directories currently installed.) Removing libprotobuf32:amd64 (3.21.12-3) ... Selecting previously unselected package libprotobuf32t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60767 files and directories currently installed.) Preparing to unpack .../libprotobuf32t64_3.21.12-8.2_amd64.deb ... Unpacking libprotobuf32t64:amd64 (3.21.12-8.2) ... Preparing to unpack .../r-cran-fs_1.6.3+dfsg-1+b1_amd64.deb ... Unpacking r-cran-fs (1.6.3+dfsg-1+b1) over (1.6.1+dfsg-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60775 files and directories currently installed.) Removing libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package libuv1t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60769 files and directories currently installed.) Preparing to unpack .../libuv1t64_1.48.0-1.1_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-1.1) ... Preparing to unpack .../mount_2.39.3-11_amd64.deb ... Unpacking mount (2.39.3-11) over (2.38.1-5+b1) ... Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) over (2.0-2.1) ... Setting up libpython3.11-minimal:amd64 (3.11.8-3+b2) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-3+b2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60775 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) over (3.11.2-1+b1) ... Setting up python3-minimal (3.11.8-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60774 files and directories currently installed.) Preparing to unpack .../python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) over (3.11.2-1+b1) ... Preparing to unpack .../libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) over (3.11.2-1+b1) ... Preparing to unpack .../libpam-runtime_1.5.3-6_all.deb ... Unpacking libpam-runtime (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 60771 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-1_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-1) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-1) ... (Reading database ... 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Setting up kallisto (0.48.0+dfsg-4+b1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.8-3+b2) ... Setting up libglx-mesa0:amd64 (24.0.3-1+b1) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b1) ... Setting up python3 (3.11.8-1) ... Setting up rna-star (2.7.11b+dfsg-1+b1) ... Setting up samtools (1.19.2-1+b1) ... Setting up bowtie2 (2.5.2-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up salmon (1.10.2+ds1-1+b2) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up jellyfish (2.3.1-3) ... Setting up r-base-core (4.3.3-3+b1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-biasedurn (2.0.11-1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-ps (1.7.6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-xml (3.99-0.16.1-1) ... Setting up hisat2 (2.2.1-4+b3) ... Setting up libnsl-dev:amd64 (1.3.0-3+b1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-locfit (1.5-9.8-1) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up rsem (1.3.3+dfsg-3+b1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Setting up r-cran-fastcluster (1.2.6-1) ... Setting up r-cran-filelock (1.0.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.11-2) ... Setting up r-cran-littler (0.3.20-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up transdecoder (5.7.1-2) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.3+dfsg-1+b1) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up r-cran-curl (5.2.0+dfsg-1+b1) ... Setting up r-cran-brio (1.1.4-1) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... 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Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ... Setting up r-cran-askpass (1.2.0-1) ... Setting up r-cran-png (0.1-8-1+b1) ... Setting up r-bioc-biobase (2.62.0-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-rstudioapi (0.16.0-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.3-1) ... Setting up r-bioc-rots (1.30.0-1) ... Setting up r-cran-cpp11 (0.4.7-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-bioc-limma (3.58.1+dfsg-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up r-bioc-tximport (1.30.0+dfsg-1) ... Setting up r-cran-kernsmooth (2.23-22-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-cachem (1.0.8-1) ... Setting up r-cran-rcpparmadillo (0.12.8.1.0-1) ... Setting up r-bioc-iranges (2.36.0-1) ... Setting up r-bioc-ctc (1.76.0-1) ... Setting up r-cran-tzdb (0.4.0-2) ... Setting up python3-htseq (2.0.5-1) ... Setting up r-cran-gdata (3.0.0-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-openssl (2.1.1+dfsg-2+b1) ... Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biocparallel (1.36.0-1) ... Setting up r-cran-callr (3.7.5-1) ... Setting up r-bioc-edger (4.0.16+dfsg-1) ... Setting up r-bioc-rhtslib (2.4.1+dfsg-3) ... Setting up r-cran-desc (1.4.3-1) ... Setting up r-cran-xml2 (1.3.6-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-survival (3.5-8-1) ... Setting up r-bioc-biocio (1.12.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-waldo (0.5.2-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.42.0-1) ... Setting up r-cran-pkgbuild (1.4.3-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up r-cran-gplots (3.1.3.1-1) ... Setting up r-cran-rsqlite (2.3.4-1) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-pkgload (1.3.4-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ... Setting up r-bioc-biostrings (2.70.3+dfsg-1) ... Setting up r-cran-testthat (3.2.1-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-bioc-rsamtools (2.18.0+dfsg-1+b1) ... Setting up r-bioc-qvalue (2.34.0-1) ... Setting up r-cran-dbplyr (2.4.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... Setting up r-bioc-biocfilecache (2.10.1+dfsg-1) ... Setting up r-bioc-keggrest (1.42.0+dfsg-1) ... Setting up r-bioc-deseq2 (1.42.1+dfsg-1) ... Setting up r-bioc-annotationdbi (1.64.1-1) ... Setting up r-bioc-go.db (3.18.0-1) ... Setting up r-bioc-annotate (1.80.0+dfsg-1) ... Setting up r-bioc-biomart (2.58.2+dfsg-1) ... Setting up r-bioc-genefilter (1.84.0-1) ... Setting up r-bioc-genomicalignments (1.38.2-1) ... Setting up r-bioc-geneplotter (1.80.0+dfsg-1) ... Setting up r-bioc-rtracklayer (1.62.0-1) ... Setting up r-bioc-genomicfeatures (1.54.3+dfsg-1) ... Setting up r-bioc-dexseq (1.48.0+dfsg-1) ... Setting up r-bioc-genelendatabase (1.38.0-1) ... Setting up r-bioc-goseq (1.54.0-1) ... Setting up libwww-perl (6.77-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for debianutils (5.17) ... Processing triggers for ca-certificates-java (20240118) ... done. Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11~7ea-1) ... Setting up openjdk-11-jre:amd64 (11.0.23~7ea-1) ... Setting up jaligner (1.0+dfsg-11) ... Setting up default-jre (2:1.17-75) ... Setting up trinityrnaseq (2.15.1+dfsg-5+b1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 5m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-yf', 'dist-upgrade'] 5m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m48.5s DUMP: 03fe75764183fb310f7b56942e7e3b94 - 5m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 5m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 5m48.8s DUMP: Package: trinityrnaseq Source: trinityrnaseq (2.15.1+dfsg-5) Version: 2.15.1+dfsg-5+b1 Installed-Size: 7456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: https://github.com/trinityrnaseq/trinityrnaseq Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.1+dfsg-5+b1_amd64.deb Size: 1720124 MD5sum: 091e1c91e745d24db55e1cc6ae5a33dc SHA256: 26095fdfb867b2e1976033be1d8a0e722cd129b4027f8f554bc381c88628464d 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 5m48.8s INFO: apt-cache knows about the following packages: trinityrnaseq 5m48.8s INFO: Running scripts pre_install 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 5m48.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 5m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 5m48.9s DUMP: trinityrnaseq: Installed: 2.15.1+dfsg-5+b1 Candidate: 2.15.1+dfsg-5+b1 Version table: *** 2.15.1+dfsg-5+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 5m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq'] 5m49.7s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.15.1+dfsg-5+b1). The following packages were automatically installed and are no longer required: fonts-font-awesome fonts-lato gcc-11-base gcc-12-base libapache-pom-java libasan6 libbamtools2.5.1 libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libgcc-10-dev libgcc-12-dev libglib2.0-0 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnsl-dev libperl5.32 libperl5.36 libprotobuf23 libpython3.9-minimal libpython3.9-stdlib libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libvecmath-java libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis sphinx-rtd-theme-common Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq'] 5m49.7s INFO: Running scripts post_install 5m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 5m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 5m49.7s INFO: Running scripts post_distupgrade 5m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_base_cleanup'] 5m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_exceptions'] 5m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_exceptions'] 5m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 5m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_squeeze-backports'] 5m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_zz_backports'] 5m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_distupgrade_zz_backports'] 5m49.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m51.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m51.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m53.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m53.9s INFO: Running scripts pre_install 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 5m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_database-server'] 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 5m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_exceptions'] 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 5m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_extras'] 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 5m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture'] 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_install_foreign_architecture_i386'] 5m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 5m54.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 5m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy'] 5m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 5m54.0s DUMP: trinityrnaseq: Installed: 2.15.1+dfsg-5+b1 Candidate: 2.15.1+dfsg-5+b1 Version table: *** 2.15.1+dfsg-5+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 5m54.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-cache', 'policy', 'trinityrnaseq'] 5m54.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq=2.15.1+dfsg-5+b1'] 5m54.7s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.15.1+dfsg-5+b1). The following packages were automatically installed and are no longer required: fonts-font-awesome fonts-lato gcc-11-base gcc-12-base libapache-pom-java libasan6 libbamtools2.5.1 libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-program-options1.74.0 libboost-thread1.74.0 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libgcc-10-dev libgcc-12-dev libglib2.0-0 libicu67 libldap-2.4-2 libllvm11 libllvm15 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libnsl-dev libperl5.32 libperl5.36 libprotobuf23 libpython3.9-minimal libpython3.9-stdlib libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libvecmath-java libwebp6 openjdk-11-jre openjdk-11-jre-headless perl-modules-5.32 perl-modules-5.36 python3.9 python3.9-minimal r-cran-assertthat r-cran-ellipsis sphinx-rtd-theme-common Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 5m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', '-y', 'install', 'trinityrnaseq=2.15.1+dfsg-5+b1'] 5m54.7s INFO: Running scripts post_install 5m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 5m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_install_exceptions'] 5m54.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m57.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 5m57.2s INFO: /bin converted to /usr/bin by /usr merge 5m57.2s INFO: /lib converted to /usr/lib by /usr merge 5m57.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 5m57.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 5m57.2s INFO: /sbin converted to /usr/sbin by /usr merge 6m0.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', '-ac', '--ignore-obsolete'] 6m11.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', '-ac', '--ignore-obsolete'] 6m11.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 6m11.1s DUMP: 0.15.6 6m11.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 6m11.1s INFO: Running adequate version 0.15.6 now. 6m11.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'trinityrnaseq'] 6m11.4s DUMP: trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 6m11.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'trinityrnaseq'] 6m11.4s ERROR: WARN: Inadequate results from running adequate! trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 6m11.4s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 6m11.4s INFO: Running scripts pre_remove 6m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 6m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 6m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 6m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 6m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 6m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 6m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 6m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 6m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 6m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 6m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_exceptions'] 6m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/pre_remove_exceptions'] 6m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 6m25.8s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46.0-1 install ok installed apt apt 2.7.14 install ok installed at-spi2-common at-spi2-common 2.51.90-4 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed berkeley-express berkeley-express 1.5.3+dfsg-3+b3 install ok installed bowtie bowtie 1.3.1-3 install ok installed bowtie2 bowtie2 2.5.2-1 install ok installed bsdutils bsdutils 1:2.39.3-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3.1 install ok installed curl curl 8.6.0-4 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed default-jre default-jre 2:1.17-75 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-11-base:amd64 gcc-11-base 11.4.0-7 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-15 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-21 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240315-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gmap gmap 2024-02-22+ds-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.41-4 install ok installed gzip gzip 1.12-1.1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hisat2 hisat2 2.2.1-4+b3 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed jaligner jaligner 1.0+dfsg-11 install ok installed java-common java-common 0.75 install ok installed jellyfish jellyfish 2.3.1-3 install ok installed kallisto kallisto 0.48.0+dfsg-4+b1 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libasan6:amd64 libasan6 11.4.0-7 install ok installed libasan8:amd64 libasan8 14-20240315-1 install ok installed libasound2-data libasound2-data 1.2.11-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.11-1+b1 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-5 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.51.90-4 install ok installed libatomic1:amd64 libatomic1 14-20240315-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b2 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b2 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-9 install ok installed libbamtools2.5.2:amd64 libbamtools2.5.2 2.5.2+dfsg-5 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-11 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost-filesystem1.74.0:amd64 libboost-filesystem1.74.0 1.74.0+ds1-23.1+b1 install ok installed libboost-filesystem1.83.0:amd64 libboost-filesystem1.83.0 1.83.0-2.1+b1 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0+ds1-23.1+b1 install ok installed libboost-iostreams1.83.0:amd64 libboost-iostreams1.83.0 1.83.0-2.1+b1 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0+ds1-23.1+b1 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-2.1+b1 install ok installed libboost-thread1.74.0:amd64 libboost-thread1.74.0 1.74.0+ds1-23.1+b1 install ok installed libboost-thread1.83.0:amd64 libboost-thread1.83.0 1.83.0-2.1+b1 install ok installed 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libconcurrent-java 1.3.4-6 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcups2t64:amd64 libcups2t64 2.4.7-1.2+b1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.6.0-4 install ok installed libcurl4t64:amd64 libcurl4t64 8.6.0-4 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.120-2 install ok installed libdrm-common libdrm-common 2.4.120-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.120-2 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.120-2 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.120-2 install ok installed libdrm2:amd64 libdrm2 2.4.120-2 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libelf1t64:amd64 libelf1t64 0.191-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b2 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-10-dev:amd64 libgcc-10-dev 10.5.0-3 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.3.0-15 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-21 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240315-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1+b1 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-3+b2 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-3 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-6 install ok installed libgfortran5:amd64 libgfortran5 14-20240315-1 install ok installed libgif7:amd64 libgif7 5.2.2-1 install ok installed libgl1:amd64 libgl1 1.7.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.0.3-1+b1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.0.3-1+b1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-6 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-6 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.0.3-1+b1 install ok installed libglx0:amd64 libglx0 1.7.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1+b1 install ok installed libgomp1:amd64 libgomp1 14-20240315-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 deinstall ok config-files libgtk2.0-0:amd64 libgtk2.0-0 2.24.33-2 install ok installed libgtk2.0-0t64:amd64 libgtk2.0-0t64 2.24.33-4 install ok installed libgtk2.0-common libgtk2.0-common 2.24.33-4 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.82-1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.24-1 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 6.45-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libhwasan0:amd64 libhwasan0 14-20240315-1 install ok installed libhwloc15:amd64 libhwloc15 2.10.0-1+b1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.085-1 install ok installed libitm1:amd64 libitm1 14-20240315-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjbzip2-java libjbzip2-java 0.9.1-8 install ok installed libjellyfish-2.0-2:amd64 libjellyfish-2.0-2 2.3.1-3 install ok installed libjemalloc2:amd64 libjemalloc2 5.3.0-2+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-6 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-11 install ok installed libjung-free-java libjung-free-java 2.1.1-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed libllvm11:amd64 libllvm11 1:11.0.1-2 install ok installed libllvm15:amd64 libllvm15 1:15.0.7-11 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-9 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblsan0:amd64 liblsan0 14-20240315-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.14-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedcrypto7t64:amd64 libmbedcrypto7t64 2.28.7-1.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedtls14t64:amd64 libmbedtls14t64 2.28.7-1.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmbedx509-1t64:amd64 libmbedx509-1t64 2.28.7-1.1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-11 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1+b1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b1 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.99-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.1+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.1+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.1+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 0.17-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15+b1 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.3-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-3 install ok installed libprotobuf23:amd64 libprotobuf23 3.12.4-1+deb11u1 install ok installed libprotobuf32t64:amd64 libprotobuf32t64 3.21.12-8.2 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3+b2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3+b2 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 14-20240315-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed libregexp-ipv6-perl libregexp-ipv6-perl 0.03-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsensors-config libsensors-config 1:3.6.0-9 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-9 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.2-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstaden-read14t64:amd64 libstaden-read14t64 1.15.0-1.1+b1 install ok installed libstdc++-10-dev:amd64 libstdc++-10-dev 10.5.0-3 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.3.0-15 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-21 install ok installed libstdc++6:amd64 libstdc++6 14-20240315-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtbb12:amd64 libtbb12 2021.11.0-2 install ok installed libtbbbind-2-5:amd64 libtbbbind-2-5 2021.11.0-2 install ok installed libtbbmalloc2:amd64 libtbbmalloc2 2021.11.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.2 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.2 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.2 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libtsan0:amd64 libtsan0 11.4.0-7 install ok installed libtsan2:amd64 libtsan2 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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+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 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 0.8.2-2+b1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.7.9-2 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed lsb-base lsb-base 11.6 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-11 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-2 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.23~7ea-1 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.23~7ea-1 install ok installed openjdk-17-jre:amd64 openjdk-17-jre 17.0.11~7ea-1 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.11~7ea-1 install ok installed openssl openssl 3.1.5-1.1 install ok installed parafly parafly 0.1.0-4 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b2 install ok installed python3 python3 3.11.8-1 install ok installed python3-hisat2 python3-hisat2 2.2.1-4 install ok installed python3-htseq python3-htseq 2.0.5-1 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-6 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b2 install ok installed python3.11 python3.11 3.11.8-3+b2 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3+b2 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed r-base-core r-base-core 4.3.3-3+b1 install ok installed r-bioc-annotate r-bioc-annotate 1.80.0+dfsg-1 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.64.1-1 install ok installed r-bioc-biobase r-bioc-biobase 2.62.0-1 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.10.1+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.48.1-2 install ok installed r-bioc-biocio r-bioc-biocio 1.12.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.36.0-1 install ok installed r-bioc-biomart r-bioc-biomart 2.58.2+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.70.3+dfsg-1 install ok installed r-bioc-ctc r-bioc-ctc 1.76.0-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.28.0+dfsg-1 install ok installed r-bioc-deseq2 r-bioc-deseq2 1.42.1+dfsg-1 install ok installed r-bioc-dexseq r-bioc-dexseq 1.48.0+dfsg-1 install ok installed r-bioc-edger r-bioc-edger 4.0.16+dfsg-1 install ok installed r-bioc-genefilter r-bioc-genefilter 1.84.0-1 install ok installed r-bioc-genelendatabase r-bioc-genelendatabase 1.38.0-1 install ok installed r-bioc-geneplotter r-bioc-geneplotter 1.80.0+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.38.6+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.11-2 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.38.2-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.54.3+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.54.1+dfsg-1 install ok installed r-bioc-go.db r-bioc-go.db 3.18.0-1 install ok installed r-bioc-goseq r-bioc-goseq 1.54.0-1 install ok installed r-bioc-iranges r-bioc-iranges 2.36.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.42.0+dfsg-1 install ok installed r-bioc-limma r-bioc-limma 3.58.1+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.14.0-1 install ok installed r-bioc-qvalue r-bioc-qvalue 2.34.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.4.1+dfsg-3 install ok installed r-bioc-rots r-bioc-rots 1.30.0-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.18.0+dfsg-1+b1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.62.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.2.0+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.40.2+dfsg-1 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.2.4+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.32.0+dfsg-1 install ok installed r-bioc-tximport r-bioc-tximport 1.30.0+dfsg-1 install ok installed r-bioc-xvector r-bioc-xvector 0.42.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.48.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 install ok installed r-cran-amap r-cran-amap 0.8-19-1 install ok installed r-cran-ape r-cran-ape 5.7-1-1 install ok installed r-cran-argparse r-cran-argparse 2.2.2+dfsg-1 install ok installed r-cran-askpass r-cran-askpass 1.2.0-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-biasedurn r-cran-biasedurn 2.0.11-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-brio r-cran-brio 1.1.4-1 install ok installed r-cran-cachem r-cran-cachem 1.0.8-1 install ok installed r-cran-callr r-cran-callr 3.7.5-1 install ok installed r-cran-catools r-cran-catools 1.18.2-1+b1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-clipr r-cran-clipr 0.8.0-1 install ok installed r-cran-cluster r-cran-cluster 2.1.6-1 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-cpp11 r-cran-cpp11 0.4.7-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.2.0+dfsg-1+b1 install ok installed r-cran-dbi r-cran-dbi 1.2.2-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.4.0+dfsg-1 install ok installed r-cran-desc r-cran-desc 1.4.3-1 install ok installed r-cran-diffobj r-cran-diffobj 0.3.5-1+b1 install ok installed r-cran-digest r-cran-digest 0.6.35-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 0.23-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-fastcluster r-cran-fastcluster 1.2.6-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-filelock r-cran-filelock 1.0.3-1 install ok installed r-cran-findpython r-cran-findpython 1.0.8-1 install ok installed r-cran-formatr r-cran-formatr 1.14-1 install ok installed r-cran-fs r-cran-fs 1.6.3+dfsg-1+b1 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-gdata r-cran-gdata 3.0.0-1 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-ggdendro r-cran-ggdendro 0.1.23+dfsg-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.4.4+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-goplot r-cran-goplot 1.0.2-2 install ok installed r-cran-gplots r-cran-gplots 3.1.3.1-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.4+dfsg-1 install ok installed r-cran-gtools r-cran-gtools 3.9.5-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-hwriter r-cran-hwriter 1.3.2.1-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-22-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-locfit r-cran-locfit 1.5-9.8-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.2.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.164-1 install ok installed r-cran-openssl r-cran-openssl 2.1.1+dfsg-2+b1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.4.3-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-pkgload r-cran-pkgload 1.3.4-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-plyr r-cran-plyr 1.8.9-1 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-processx r-cran-processx 3.8.3-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-ps r-cran-ps 1.7.6-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 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 1.0.12-1 install ok installed r-cran-rcpparmadillo r-cran-rcpparmadillo 0.12.8.1.0-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.14+dfsg-1+b1 install ok installed r-cran-readr r-cran-readr 2.1.5-1 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-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.4-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.4-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.16.0-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-statmod r-cran-statmod 1.5.0-1 install ok installed r-cran-stringi r-cran-stringi 1.8.3-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-survival r-cran-survival 3.5-8-1 install ok installed r-cran-sys r-cran-sys 3.4.2-1 install ok installed r-cran-testthat r-cran-testthat 3.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-tzdb r-cran-tzdb 0.4.0-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-vroom r-cran-vroom 1.6.5-1 install ok installed r-cran-waldo r-cran-waldo 0.5.2-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.16.1-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.6-1 install ok installed r-cran-xtable r-cran-xtable 1:1.8-4-2 install ok installed r-cran-yaml r-cran-yaml 2.3.8-1 install ok installed readline-common readline-common 8.2-4 install ok installed rna-star rna-star 2.7.11b+dfsg-1+b1 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed rsem rsem 1.3.3+dfsg-3+b1 install ok installed salmon salmon 1.10.2+ds1-1+b2 install ok installed samtools samtools 1.19.2-1+b1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed shared-mime-info shared-mime-info 2.4-3 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 2.0.0+dfsg-1 install ok installed subread subread 2.0.6+dfsg-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed transdecoder transdecoder 5.7.1-2 install ok installed trimmomatic trimmomatic 0.39+dfsg-2 install ok installed trinityrnaseq trinityrnaseq 2.15.1+dfsg-5+b1 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-11 install ok installed util-linux-extra util-linux-extra 2.39.3-11 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 zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3.1 6m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 6m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'remove', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'gmap', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapache-pom-java', 'libasan6:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libelf1t64:amd64', 'libencode-locale-perl', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libjsr305-java', 'libjung-free-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls12:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1t64:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libprotobuf23:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libregexp-ipv6-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libvecmath-java', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', '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', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'node-html5shiv', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parafly', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'python3', 'python3-hisat2', 'python3-htseq', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-ctc', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-dexseq', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genelendatabase', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-go.db', 'r-bioc-goseq', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-qvalue', 'r-bioc-rhtslib', 'r-bioc-rots', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-amap', 'r-cran-ape', 'r-cran-argparse', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-biasedurn', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-catools', 'r-cran-cli', 'r-cran-clipr', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastcluster', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-findpython', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-gdata', 'r-cran-generics', 'r-cran-ggdendro', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-goplot', 'r-cran-gplots', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-gtools', 'r-cran-hms', 'r-cran-httr', 'r-cran-hwriter', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', '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-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rna-star', 'rpcsvc-proto', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'shared-mime-info', 'sphinx-rtd-theme-common', 'subread', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'trinityrnaseq'] 6m33.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Package 'libgtk2.0-0' is not installed, so not removed The following packages were automatically installed and are no longer required: gcc-12-base libperl5.36 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato gcc-11-base gcc-13-base gmap gtk-update-icon-cache hicolor-icon-theme hisat2 jaligner java-common jellyfish kallisto libapache-pom-java libasan6 libasan8 libasound2-data libasound2t64 libatinject-jsr330-api-java libatk1.0-0t64 libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libbamtools2.5.2 libblas3 libboost-dev libboost-filesystem1.74.0 libboost-filesystem1.83.0 libboost-iostreams1.74.0 libboost-iostreams1.83.0 libboost-program-options1.74.0 libboost-program-options1.83.0 libboost-thread1.74.0 libboost-thread1.83.0 libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libclone-perl libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libencode-locale-perl liberror-prone-java libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-13-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgtk2.0-0t64 libgtk2.0-common libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwasan0 libhwloc15 libice6 libicu67 libicu72 libio-html-perl libio-socket-ssl-perl libitm1 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore libjsr305-java libjung-free-java liblapack3 liblcms2-2 libldap-2.4-2 libldap-2.5-0 liblerc4 libllvm11 libllvm15 libllvm17t64 liblmdb0 liblsan0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedcrypto7t64 libmbedtls12 libmbedtls14t64 libmbedx509-0 libmbedx509-1t64 libmpdec3 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnsl-dev libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.32 libpixman-1-0 libpng16-16t64 libprotobuf23 libprotobuf32t64 libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8t64 libregexp-ipv6-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libstaden-read14t64 libstdc++-10-dev libstdc++-12-dev libstdc++-13-dev libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libthai-data libthai0 libtiff5 libtiff6 libtimedate-perl libtirpc-dev libtk8.6 libtry-tiny-perl libtsan0 libtsan2 libubsan1 liburi-perl libuv1t64 libvecmath-java libvulkan1 libwebp6 libwebp7 libwww-perl libwww-robotrules-perl 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 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev littler media-types ncbi-blast+ ncbi-data netbase node-html5shiv openjdk-11-jre openjdk-11-jre-headless openjdk-17-jre openjdk-17-jre-headless openssl parafly perl-modules-5.32 perl-openssl-defaults python3 python3-hisat2 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.11 python3.11-minimal python3.9 python3.9-minimal r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-ctc r-bioc-delayedarray r-bioc-deseq2 r-bioc-dexseq r-bioc-edger r-bioc-genefilter r-bioc-genelendatabase r-bioc-geneplotter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-go.db r-bioc-goseq r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-qvalue r-bioc-rhtslib r-bioc-rots r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-amap r-cran-ape r-cran-argparse r-cran-askpass r-cran-assertthat r-cran-bh r-cran-biasedurn r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-catools r-cran-cli r-cran-clipr r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastcluster r-cran-fastmap r-cran-filelock r-cran-findpython r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-gdata r-cran-generics r-cran-ggdendro r-cran-ggplot2 r-cran-glue r-cran-goplot r-cran-gplots r-cran-gridextra r-cran-gtable r-cran-gtools r-cran-hms r-cran-httr r-cran-hwriter r-cran-isoband r-cran-jsonlite r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-png r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-reshape2 r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow 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-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rna-star rpcsvc-proto rsem salmon samtools sensible-utils shared-mime-info sphinx-rtd-theme-common subread transdecoder trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 458 to remove and 0 not upgraded. After this operation, 2472 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 ... 61154 files and directories currently installed.) Removing trinityrnaseq (2.15.1+dfsg-5+b1) ... Removing trimmomatic (0.39+dfsg-2) ... Removing default-jre (2:1.17-75) ... Removing openjdk-17-jre:amd64 (17.0.11~7ea-1) ... Removing libgtk2.0-0t64:amd64 (2.24.33-4) ... Removing adwaita-icon-theme (46.0-1) ... Removing libatk1.0-0t64:amd64 (2.51.90-4) ... Removing at-spi2-common (2.51.90-4) ... Removing berkeley-express (1.5.3+dfsg-3+b3) ... Removing rsem (1.3.3+dfsg-3+b1) ... Removing bowtie (1.3.1-3) ... Removing bowtie2 (2.5.2-1) ... Removing r-cran-goplot (1.0.2-2) ... Removing r-cran-ggdendro (0.1.23+dfsg-1) ... Removing r-bioc-goseq (1.54.0-1) ... Removing r-bioc-genelendatabase (1.38.0-1) ... Removing r-bioc-genomicfeatures (1.54.3+dfsg-1) ... Removing r-bioc-rtracklayer (1.62.0-1) ... Removing r-bioc-genomicalignments (1.38.2-1) ... Removing r-bioc-dexseq (1.48.0+dfsg-1) ... Removing transdecoder (5.7.1-2) ... Removing r-bioc-genefilter (1.84.0-1) ... Removing r-cran-survival (3.5-8-1) ... Removing openjdk-11-jre:amd64 (11.0.23~7ea-1) ... Removing libconcurrent-java (1.3.4-6) ... Removing openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) ... Removing curl (8.6.0-4) ... Removing jaligner (1.0+dfsg-11) ... Removing default-jre-headless (2:1.17-75) ... Removing sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... dpkg: warning: while removing fonts-lato, directory '/usr/share/fonts/truetype/lato' not empty so not removed Removing libstdc++-10-dev:amd64 (10.5.0-3) ... Removing libgcc-10-dev:amd64 (10.5.0-3) ... Removing libtsan0:amd64 (11.4.0-7) ... Removing libasan6:amd64 (11.4.0-7) ... Removing gcc-11-base:amd64 (11.4.0-7) ... Removing r-bioc-rsamtools (2.18.0+dfsg-1+b1) ... Removing r-bioc-deseq2 (1.42.1+dfsg-1) ... Removing r-bioc-biocparallel (1.36.0-1) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-2.1+b1) ... Removing libstdc++-13-dev:amd64 (13.2.0-21) ... Removing libgcc-13-dev:amd64 (13.2.0-21) ... Removing gcc-13-base:amd64 (13.2.0-21) ... Removing gmap (2024-02-22+ds-1) ... Removing gtk-update-icon-cache (3.24.41-4) ... Removing hicolor-icon-theme (0.17-2) ... Removing python3-hisat2 (2.2.1-4) ... Removing hisat2 (2.2.1-4+b3) ... Removing openjdk-17-jre-headless:amd64 (17.0.11~7ea-1) ... Removing java-common (0.75) ... Removing jellyfish (2.3.1-3) ... Removing kallisto (0.48.0+dfsg-4+b1) ... Removing libcommons-collections4-java (4.4-2) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing libstdc++-12-dev:amd64 (12.3.0-15) ... Removing libgcc-12-dev:amd64 (12.3.0-15) ... Removing libasan8:amd64 (14-20240315-1) ... Removing libasound2t64:amd64 (1.2.11-1+b1) ... Removing libasound2-data (1.2.11-1) ... Removing libjung-free-java (2.1.1-2) ... Removing libatomic1:amd64 (14-20240315-1) ... Removing libcups2t64:amd64 (2.4.7-1.2+b1) ... Removing libavahi-client3:amd64 (0.8-13+b2) ... Removing libavahi-common3:amd64 (0.8-13+b2) ... Removing libavahi-common-data:amd64 (0.8-13+b2) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-9) ... Removing libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Removing r-cran-rcpparmadillo (0.12.8.1.0-1) ... Removing r-bioc-edger (4.0.16+dfsg-1) ... Removing python3-htseq (2.0.5-1) ... Removing python3-numpy (1:1.26.4+ds-6) ... Removing libboost-filesystem1.74.0:amd64 (1.74.0+ds1-23.1+b1) ... Removing salmon (1.10.2+ds1-1+b2) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-2.1+b1) ... Removing libboost-iostreams1.74.0:amd64 (1.74.0+ds1-23.1+b1) ... Removing libboost-iostreams1.83.0:amd64 (1.83.0-2.1+b1) ... Removing libboost-program-options1.74.0:amd64 (1.74.0+ds1-23.1+b1) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-2.1+b1) ... Removing libboost-thread1.74.0:amd64 (1.74.0+ds1-23.1+b1) ... Removing libboost-thread1.83.0:amd64 (1.83.0-2.1+b1) ... Removing r-bioc-geneplotter (1.80.0+dfsg-1) ... Removing r-bioc-annotate (1.80.0+dfsg-1) ... Removing libgl1:amd64 (1.7.0-1) ... Removing libglx0:amd64 (1.7.0-1) ... Removing libglx-mesa0:amd64 (24.0.3-1+b1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing r-bioc-go.db (3.18.0-1) ... Removing r-bioc-biomart (2.58.2+dfsg-1) ... Removing r-bioc-annotationdbi (1.64.1-1) ... Removing r-bioc-keggrest (1.42.0+dfsg-1) ... Removing r-bioc-biostrings (2.70.3+dfsg-1) ... Removing r-bioc-rhtslib (2.4.1+dfsg-3) ... Removing libcolt-free-java (1.2.0+dfsg-8) ... Removing libstaden-read14t64:amd64 (1.15.0-1.1+b1) ... Removing samtools (1.19.2-1+b1) ... Removing libdbus-1-3:amd64 (1.14.10-4+b1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b2) ... Removing libgl1-mesa-dri:amd64 (24.0.3-1+b1) ... Removing libdrm-amdgpu1:amd64 (2.4.120-2) ... Removing libdrm-radeon1:amd64 (2.4.120-2) ... Removing libdrm-nouveau2:amd64 (2.4.120-2) ... Removing libdrm-intel1:amd64 (2.4.120-2) ... Removing libllvm11:amd64 (1:11.0.1-2) ... Removing libllvm17t64:amd64 (1:17.0.6-9) ... Removing libelf1t64:amd64 (0.191-1) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing r-cran-argparse (2.2.2+dfsg-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Removing libgetopt-java (1.0.14+dfsg-6) ... Removing r-cran-ape (5.7-1-1) ... Removing libgif7:amd64 (5.2.2-1) ... Removing libglapi-mesa:amd64 (24.0.3-1+b1) ... Removing libglib2.0-0:amd64 (2.78.4-6) ... Removing shared-mime-info (2.4-3) ... Removing libglvnd0:amd64 (1.7.0-1) ... Removing rna-star (2.7.11b+dfsg-1+b1) ... Removing parafly (0.1.0-4) ... Removing libgtk2.0-common (2.24.33-4) ... Removing libhwasan0:amd64 (14-20240315-1) ... Removing libtbb12:amd64 (2021.11.0-2) ... Removing libtbbbind-2-5:amd64 (2021.11.0-2) ... Removing libhwloc15:amd64 (2.10.0-1+b1) ... Removing libicu67:amd64 (67.1-7) ... Removing r-bioc-biocfilecache (2.10.1+dfsg-1) ... Removing r-cran-dbplyr (2.4.0+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-bioc-qvalue (2.34.0-1) ... Removing r-cran-reshape2 (1.4.4-2) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.3-1) ... Removing r-cran-xml2 (1.3.6-1) ... Removing libitm1:amd64 (14-20240315-1) ... Removing libjbzip2-java (0.9.1-8) ... Removing libjellyfish-2.0-2:amd64 (2.3.1-3) ... Removing libjemalloc2:amd64 (5.3.0-2+b1) ... Removing libjs-sphinxdoc (7.2.6-6) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libllvm15:amd64 (1:15.0.7-11) ... Removing ncbi-blast+ (2.12.0+ds-4+b1) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... Removing liblsan0:amd64 (14-20240315-1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libmbedtls14t64:amd64 (2.28.7-1.1) ... Removing libmbedx509-1t64:amd64 (2.28.7-1.1) ... Removing libmbedcrypto7t64:amd64 (2.28.7-1.1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libnsl-dev:amd64 (1.3.0-3+b1) ... Removing libnss3:amd64 (2:3.99-1) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libpciaccess0:amd64 (0.17-3) ... Removing libpcsclite1:amd64 (2.0.3-1) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing r-cran-png (0.1-8-1+b1) ... Removing libprotobuf23:amd64 (3.12.4-1+deb11u1) ... Removing libprotobuf32t64:amd64 (3.21.12-8.2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libquadmath0:amd64 (14-20240315-1) ... Removing libregexp-ipv6-perl (0.03-3) ... Removing libsensors5:amd64 (1:3.6.0-9) ... Removing libsensors-config (1:3.6.0-9) ... Removing libtbbmalloc2:amd64 (2021.11.0-2) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.2) ... Removing libtsan2:amd64 (14-20240315-1) ... Removing libubsan1:amd64 (14-20240315-1) ... Removing r-cran-testthat (3.2.1-1) ... Removing r-cran-pkgload (1.3.4-1) ... Removing r-cran-fs (1.6.3+dfsg-1+b1) ... Removing libuv1t64:amd64 (1.48.0-1.1) ... Removing libvecmath-java (1.5.2-7) ... Removing libvulkan1:amd64 (1.3.275.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-xcb1:amd64 (2:1.8.7-1) ... Removing libxcb-dri2-0:amd64 (1.15-1) ... Removing libxcb-dri3-0:amd64 (1.15-1) ... Removing libxcb-glx0:amd64 (1.15-1) ... Removing libxcb-present0:amd64 (1.15-1) ... Removing libxcb-randr0:amd64 (1.15-1) ... Removing libxcb-sync1:amd64 (1.15-1) ... Removing libxcb-xfixes0:amd64 (1.15-1) ... Removing libxcomposite1:amd64 (1:0.4.5-1) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxdamage1:amd64 (1:1.1.6-1) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxrandr2:amd64 (2:1.5.4-1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing r-cran-readr (2.1.5-1) ... Removing littler (0.3.20-1) ... Removing ncbi-data (6.1.20170106+dfsg2-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing python3-pysam (0.22.0+ds-1+b2) ... Removing r-bioc-rots (1.30.0-1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-bioc-tximport (1.30.0+dfsg-1) ... Removing r-bioc-biocio (1.12.0+dfsg-1) ... Removing r-bioc-ctc (1.76.0-1) ... Removing r-bioc-limma (3.58.1+dfsg-1) ... Removing r-cran-amap (0.8-19-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-biasedurn (2.0.11-1) ... Removing r-cran-vroom (1.6.5-1) ... Removing r-cran-rsqlite (2.3.4-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-gplots (3.1.3.1-1) ... Removing r-cran-catools (1.18.2-1+b1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-brio (1.1.4-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.8-1) ... Removing r-cran-pkgbuild (1.4.3-1) ... Removing r-cran-callr (3.7.5-1) ... Removing r-cran-waldo (0.5.2-1) ... Removing r-cran-dplyr (1.1.4-1) ... Removing r-cran-tidyselect (1.2.0+dfsg-1) ... Removing r-cran-clipr (0.8.0-1) ... Removing r-cran-cluster (2.1.6-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-tzdb (0.4.0-2) ... Removing r-cran-cpp11 (0.4.7-1) ... Removing r-cran-diffobj (0.3.5-1+b1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-dbi (1.2.2-1) ... Removing r-cran-desc (1.4.3-1) ... Removing r-cran-digest (0.6.35-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (0.23-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-fastcluster (1.2.6-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-findpython (1.0.8-1) ... 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-gdata (3.0.0-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-gtools (3.9.5-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-hwriter (1.3.2.1-1) ... Removing r-cran-kernsmooth (2.23-22-1) ... Removing r-cran-locfit (1.5-9.8-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-plyr (1.8.9-1) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-processx (3.8.3-1) ... Removing r-cran-ps (1.7.6-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-rprojroot (2.0.4-1) ... Removing r-cran-rstudioapi (0.16.0-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-statmod (1.5.0-1) ... Removing r-cran-xml (3.99-0.16.1-1) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-cran-yaml (2.3.8-1) ... Removing subread (2.0.6+dfsg-2) ... Removing r-cran-ggplot2 (3.4.4+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... Removing r-bioc-delayedarray (0.28.0+dfsg-1) ... Removing r-bioc-sparsearray (1.2.4+dfsg-1) ... Removing r-bioc-s4arrays (1.2.0+dfsg-1) ... Removing r-cran-abind (1.4-5-2) ... Removing ca-certificates-java (20240118) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-curl (5.2.0+dfsg-1+b1) ... Removing r-bioc-genomicranges (1.54.1+dfsg-1) ... Removing r-bioc-xvector (0.42.0-1) ... Removing r-bioc-zlibbioc (1.48.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libc6-dev:amd64 (2.37-15.1) ... Removing libc-dev-bin (2.37-15.1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.6.0-4) ... Removing libdrm2:amd64 (2.4.120-2) ... Removing libdrm-common (2.4.120-2) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.8-3+b2) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3+b2) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing python3-minimal (3.11.8-1) ... Removing libsqlite3-0:amd64 (3.45.2-1) ... Removing linux-libc-dev (6.7.9-2) ... Removing r-cran-rcpp (1.0.12-1) ... Removing media-types (10.1.0) ... Removing r-bioc-biobase (2.62.0-1) ... Removing r-bioc-genomeinfodb (1.38.6+dfsg-1) ... Removing r-bioc-iranges (2.36.0-1) ... Removing r-bioc-s4vectors (0.40.2+dfsg-1) ... Removing r-bioc-matrixgenerics (1.14.0-1) ... Removing r-bioc-biocgenerics (0.48.1-2) ... Removing r-bioc-genomeinfodbdata (1.2.11-2) ... Removing r-cran-openssl (2.1.1+dfsg-2+b1) ... Removing r-cran-askpass (1.2.0-1) ... Removing r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-gtable (0.3.4+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.164-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-matrixstats (1.2.0-1) ... Removing r-cran-mime (0.12-1+b1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-sys (3.4.2-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing python3.11-minimal (3.11.8-3+b2) ... Removing libpython3.11-minimal:amd64 (3.11.8-3+b2) ... find: '/usr/lib/python3': No such file or directory Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing r-cran-cli (3.6.2-1) ... Removing r-base-core (4.3.3-3+b1) ... Removing libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.1+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-3) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b2) ... Removing libcurl4t64:amd64 (8.6.0-4) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libgfortran5:amd64 (14-20240315-1) ... Removing libglib2.0-0t64:amd64 (2.78.4-6) ... Removing libgomp1:amd64 (14-20240315-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.59.0-1+b1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... 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 readline-common (8.2-4) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.12.2-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... 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 liberror-prone-java (2.18.0-1) ... Removing libguava-java (32.0.1-1) ... Removing libatinject-jsr330-api-java (1.0+ds1-5) ... Removing libwww-perl (6.77-1) ... Removing liblwp-protocol-https-perl (6.14-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.16-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.82-1) ... Removing libhtml-tagset-perl (3.24-1) ... Removing libhttp-cookies-perl (6.11-1) ... Removing libio-socket-ssl-perl (2.085-1) ... Removing libjsr305-java (0.1~+svn49-11) ... Removing libnet-http-perl (6.23-1) ... Removing libnet-ssleay-perl:amd64 (1.94-1+b1) ... Removing libtry-tiny-perl (0.31-2) ... Removing libwww-robotrules-perl (6.02-1) ... Removing netbase (6.4) ... Removing perl-openssl-defaults:amd64 (7+b2) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.45-1) ... Removing libclone-perl:amd64 (0.46-1+b2) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.06-1) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing libtimedate-perl (2.3300-2) ... Removing liburi-perl (5.27-1) ... Removing openssl (3.1.5-1.1) ... Processing triggers for libc-bin (2.37-15.1) ... 6m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'remove', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'gmap', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapache-pom-java', 'libasan6:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libelf1t64:amd64', 'libencode-locale-perl', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libjsr305-java', 'libjung-free-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls12:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1t64:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libprotobuf23:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libregexp-ipv6-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libvecmath-java', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', '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', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'node-html5shiv', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parafly', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'python3', 'python3-hisat2', 'python3-htseq', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-ctc', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-dexseq', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genelendatabase', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-go.db', 'r-bioc-goseq', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-qvalue', 'r-bioc-rhtslib', 'r-bioc-rots', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-amap', 'r-cran-ape', 'r-cran-argparse', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-biasedurn', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-catools', 'r-cran-cli', 'r-cran-clipr', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastcluster', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-findpython', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-gdata', 'r-cran-generics', 'r-cran-ggdendro', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-goplot', 'r-cran-gplots', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-gtools', 'r-cran-hms', 'r-cran-httr', 'r-cran-hwriter', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', '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-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rna-star', 'rpcsvc-proto', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'shared-mime-info', 'sphinx-rtd-theme-common', 'subread', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'trinityrnaseq'] 6m33.6s INFO: Running scripts post_remove 6m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_remove_exceptions'] 6m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_remove_exceptions'] 6m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'gmap', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapache-pom-java', 'libasan6:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libelf1t64:amd64', 'libencode-locale-perl', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libjsr305-java', 'libjung-free-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls12:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1t64:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libprotobuf23:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libregexp-ipv6-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libvecmath-java', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', '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', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'node-html5shiv', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parafly', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'python3', 'python3-hisat2', 'python3-htseq', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-ctc', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-dexseq', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genelendatabase', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-go.db', 'r-bioc-goseq', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-qvalue', 'r-bioc-rhtslib', 'r-bioc-rots', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-amap', 'r-cran-ape', 'r-cran-argparse', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-biasedurn', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-catools', 'r-cran-cli', 'r-cran-clipr', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastcluster', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-findpython', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-gdata', 'r-cran-generics', 'r-cran-ggdendro', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-goplot', 'r-cran-gplots', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-gtools', 'r-cran-hms', 'r-cran-httr', 'r-cran-hwriter', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', '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-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rna-star', 'rpcsvc-proto', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'shared-mime-info', 'sphinx-rtd-theme-common', 'subread', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 6m34.5s DUMP: (Reading database ... 9571 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (46.0-1) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove berkeley-express which isn't installed dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove curl which isn't installed dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/truetype/font-awesome' not empty so not removed dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/opentype/font-awesome' not empty so not removed dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove gcc-11-base which isn't installed dpkg: warning: ignoring request to remove gcc-13-base which isn't installed dpkg: warning: ignoring request to remove gmap which isn't installed dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed dpkg: warning: ignoring request to remove hisat2 which isn't installed dpkg: warning: ignoring request to remove jaligner which isn't installed Purging configuration files for java-common (0.75) ... dpkg: warning: ignoring request to remove jellyfish which isn't installed dpkg: warning: ignoring request to remove kallisto which isn't installed dpkg: warning: ignoring request to remove libapache-pom-java which isn't installed dpkg: warning: ignoring request to remove libasan6 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libasound2t64 which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.2 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libcolt-free-java which isn't installed dpkg: warning: ignoring request to remove libcommons-collections4-java which isn't installed dpkg: warning: ignoring request to remove libcommons-parent-java which isn't installed dpkg: warning: ignoring request to remove libconcurrent-java which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-4) ... dpkg: warning: ignoring request to remove libcups2t64 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-nouveau2 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove liberror-prone-java which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-10-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-13-dev which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b2) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgetopt-java which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (24.0.3-1+b1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed dpkg: warning: ignoring request to remove libglib2.0-0 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-6) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgtk2.0-0t64:amd64 (2.24.33-4) ... Purging configuration files for libgtk2.0-common (2.24.33-4) ... dpkg: warning: ignoring request to remove libguava-java which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjbzip2-java which isn't installed dpkg: warning: ignoring request to remove libjellyfish-2.0-2 which isn't installed dpkg: warning: ignoring request to remove libjemalloc2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libjsr305-java which isn't installed dpkg: warning: ignoring request to remove libjung-free-java which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libllvm11 which isn't installed dpkg: warning: ignoring request to remove libllvm15 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7t64 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14t64 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1t64 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libprotobuf23 which isn't installed dpkg: warning: ignoring request to remove libprotobuf32t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3+b2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove libregexp-ipv6-perl which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-9) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstaden-read14t64 which isn't installed dpkg: warning: ignoring request to remove libstdc++-10-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-dev which isn't installed dpkg: warning: ignoring request to remove libtbb12 which isn't installed dpkg: warning: ignoring request to remove libtbbbind-2-5 which isn't installed dpkg: warning: ignoring request to remove libtbbmalloc2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libtsan0 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libvecmath-java which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-randr0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-2) ... Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove openjdk-11-jre which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.23~7ea-1) ... dpkg: warning: ignoring request to remove openjdk-17-jre which isn't installed Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.11~7ea-1) ... Purging configuration files for openssl (3.1.5-1.1) ... dpkg: warning: ignoring request to remove parafly which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-hisat2 which isn't installed dpkg: warning: ignoring request to remove python3-htseq which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-3+b2) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.3.3-3+b1) ... 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-biocfilecache 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-biomart 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-ctc 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-dexseq which isn't installed dpkg: warning: ignoring request to remove r-bioc-edger which isn't installed dpkg: warning: ignoring request to remove r-bioc-genefilter which isn't installed dpkg: warning: ignoring request to remove r-bioc-genelendatabase 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-genomicfeatures 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-go.db which isn't installed dpkg: warning: ignoring request to remove r-bioc-goseq 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-limma 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-qvalue 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-rots which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-tximport which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-amap which isn't installed dpkg: warning: ignoring request to remove r-cran-ape which isn't installed dpkg: warning: ignoring request to remove r-cran-argparse 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-assertthat 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-biasedurn 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-brio 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-catools 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-cluster 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-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-curl 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-dbplyr 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 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-fastcluster 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-filelock which isn't installed dpkg: warning: ignoring request to remove r-cran-findpython 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-gdata 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-ggdendro 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-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-goplot which isn't installed dpkg: warning: ignoring request to remove r-cran-gplots 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-gtools 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-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-hwriter 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-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-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-lattice 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-littler 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-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-openssl 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-pkgbuild 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-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-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-processx 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-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-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-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-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-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-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-rstudioapi 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-snow 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-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-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 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 Purging configuration files for readline-common (8.2-4) ... dpkg: warning: ignoring request to remove rna-star which isn't installed dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove rsem 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 shared-mime-info (2.4-3) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed dpkg: warning: ignoring request to remove subread which isn't installed dpkg: warning: ignoring request to remove transdecoder which isn't installed dpkg: warning: ignoring request to remove trimmomatic which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 6m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'gmap', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'hisat2', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapache-pom-java', 'libasan6:amd64', 'libasan8:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-filesystem1.74.0:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-iostreams1.83.0:amd64', 'libboost-program-options1.74.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libelf1t64:amd64', 'libencode-locale-perl', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgtk2.0-0:amd64', 'libgtk2.0-0t64:amd64', 'libgtk2.0-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwasan0:amd64', 'libhwloc15:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libjsr305-java', 'libjung-free-java', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm11:amd64', 'libllvm15:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblsan0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls12:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1t64:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libprotobuf23:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libregexp-ipv6-perl', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libstaden-read14t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libtbb12:amd64', 'libtbbbind-2-5:amd64', 'libtbbmalloc2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'liburi-perl', 'libuv1t64:amd64', 'libvecmath-java', 'libvulkan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', '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', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'littler', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'node-html5shiv', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'parafly', 'perl-modules-5.32', 'perl-openssl-defaults:amd64', 'python3', 'python3-hisat2', 'python3-htseq', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-ctc', 'r-bioc-delayedarray', 'r-bioc-deseq2', 'r-bioc-dexseq', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genelendatabase', 'r-bioc-geneplotter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-go.db', 'r-bioc-goseq', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-qvalue', 'r-bioc-rhtslib', 'r-bioc-rots', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tximport', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-amap', 'r-cran-ape', 'r-cran-argparse', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-biasedurn', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-catools', 'r-cran-cli', 'r-cran-clipr', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastcluster', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-findpython', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-gdata', 'r-cran-generics', 'r-cran-ggdendro', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-goplot', 'r-cran-gplots', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-gtools', 'r-cran-hms', 'r-cran-httr', 'r-cran-hwriter', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcpparmadillo', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-reshape2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', '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-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rna-star', 'rpcsvc-proto', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'shared-mime-info', 'sphinx-rtd-theme-common', 'subread', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 6m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', 'trinityrnaseq'] 6m34.5s DUMP: dpkg: warning: ignoring request to remove trinityrnaseq which isn't installed 6m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', 'trinityrnaseq'] 6m34.5s INFO: Running scripts post_purge 6m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_purge_exceptions'] 6m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_purge_exceptions'] 6m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', '--pending'] 6m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--purge', '--pending'] 6m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--remove', '--pending'] 6m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg', '--remove', '--pending'] 6m34.5s INFO: Running scripts post_test 6m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_test_exceptions'] 6m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'tmp/scripts/post_test_exceptions'] 6m34.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 6m35.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 6m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-divert', '--list'] 6m35.0s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64 diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64 6m35.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'dpkg-divert', '--list'] 6m35.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'clean'] 6m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w', 'apt-get', 'clean'] 6m35.3s DEBUG: Recording chroot state 6m36.1s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-lato, fonts-dejavu-mono, fonts-dejavu-core, fonts-font-awesome /usr/share/fonts/.uuid not owned /usr/share/fonts/opentype/ owned by: fonts-font-awesome /usr/share/fonts/opentype/.uuid not owned /usr/share/fonts/opentype/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/opentype/font-awesome/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-lato, fonts-dejavu-mono, fonts-dejavu-core, fonts-font-awesome /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned /usr/share/fonts/truetype/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/truetype/font-awesome/.uuid not owned /usr/share/fonts/truetype/lato/ owned by: fonts-lato /usr/share/fonts/truetype/lato/.uuid not owned 6m36.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/shm'] 6m36.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/shm'] 6m36.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/console'] 6m36.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/console'] 6m36.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/ptmx'] 6m36.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/ptmx'] 6m36.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/pts'] 6m36.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/dev/pts'] 6m36.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/proc'] 6m36.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w/proc'] 6m36.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 6m36.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpizzr_c2w'] 6m36.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpizzr_c2w 6m36.9s INFO: PASS: Upgrading between Debian distributions. 6m36.9s INFO: PASS: All tests. 6m36.9s INFO: piuparts run ends. ret=0 End: 2024-03-27 23:38:02 GMT