Start: 2024-08-18 20:38:00 GMT [stable] Package: r-bioc-titancna Version: 1.28.0-2 Installed-Size: 7619 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-biocgenerics (>= 0.31.6), r-bioc-iranges (>= 2.6.1), r-bioc-genomicranges (>= 1.24.3), r-bioc-variantannotation (>= 1.18.7), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.8.7), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description: Subclonal copy number and LOH prediction from whole genome sequencing Homepage: https://bioconductor.org/packages/TitanCNA/ Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.28.0-2_amd64.deb Size: 3951012 MD5sum: cf977cde164b7582344ad2334c626af7 SHA256: a8d3d1c31baabf6b85862d789ee5227105be5d7b1e1e4d4ac0215b426dda13c7 [testing] Package: r-bioc-titancna Version: 1.36.0-1 Installed-Size: 7613 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-biocgenerics (>= 0.31.6), r-bioc-iranges (>= 2.6.1), r-bioc-genomicranges (>= 1.24.3), r-bioc-variantannotation (>= 1.18.7), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.8.7), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description: Subclonal copy number and LOH prediction from whole genome sequencing Homepage: https://bioconductor.org/packages/TitanCNA/ Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.36.0-1_amd64.deb Size: 3901912 MD5sum: 456c00800dd8d518f7de2f64bfda5efe SHA256: 3e9ac90131fac6333087d97e6b560b6d54ce53c00f0744e04022f06d14ffb2d3 [sid] Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description: Subclonal copy number and LOH prediction from whole genome sequencing Homepage: https://bioconductor.org/packages/TitanCNA/ Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b 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 r-bioc-titancna=1.42.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.2 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 r-bioc-titancna=1.42.0-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpds2qfkmn 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpds2qfkmn 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpds2qfkmn/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: e0568dca630aa17b9cacee75afdb778e - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s 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' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s 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+deb11u10 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+deb11u2 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+deb11u2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u10 install ok installed libc6:amd64 libc6 2.31-13+deb11u10 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+deb11u5 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+deb11u2 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+deb11u2 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+deb11u5 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+deb11u5 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 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+deb11u2 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+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m4.3s DUMP: Package: r-bioc-titancna Version: 1.28.0-2 Installed-Size: 7619 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-biocgenerics (>= 0.31.6), r-bioc-iranges (>= 2.6.1), r-bioc-genomicranges (>= 1.24.3), r-bioc-variantannotation (>= 1.18.7), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.8.7), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description-en: Subclonal copy number and LOH prediction from whole genome sequencing Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Homepage: https://bioconductor.org/packages/TitanCNA/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.28.0-2_amd64.deb Size: 3951012 MD5sum: cf977cde164b7582344ad2334c626af7 SHA256: a8d3d1c31baabf6b85862d789ee5227105be5d7b1e1e4d4ac0215b426dda13c7 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m4.3s INFO: apt-cache knows about the following packages: r-bioc-titancna 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.10,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m4.5s DUMP: r-bioc-titancna: Installed: (none) Candidate: 1.28.0-2 Version table: 1.28.0-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m42.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo libjs-jquery liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-foreach r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-iterators r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: 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 libstdc++-10-doc tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-org.hs.eg.db r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-rmarkdown r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-bbmisc r-bioc-shortread r-cran-testthat r-cran-biocmanager r-cran-runit r-bioc-hdf5array r-bioc-genefilter r-bioc-delayedmatrixstats r-bioc-edger r-bioc-ensembldb r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-limma r-bioc-rhdf5 r-cran-ggplot2 r-cran-covr r-cran-roxygen2 r-cran-callr r-cran-htmlwidgets r-cran-ps r-cran-rstudioapi r-cran-prettycode r-cran-r.utils r-cran-xts r-cran-zoo r-cran-yaml r-cran-rmysql r-cran-bench r-cran-broom r-cran-rpostgresql r-cran-unitizer r-cran-shiny r-cran-forcats r-cran-lubridate r-cran-httpuv r-cran-jpeg r-cran-png r-cran-readr r-cran-plyr r-cran-sf r-cran-getopt r-cran-base64enc r-cran-scales r-cran-inline r-cran-gh r-cran-rvest r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-evaluate r-cran-formattable r-cran-htmltools r-cran-tidyr r-cran-zeallot readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-bioc-go.db r-cran-runit r-cran-testthat r-cran-batchjobs r-cran-doparallel r-cran-batchtools r-cran-rmpi r-bioc-biovizbase r-bioc-shortread r-bioc-annotate r-bioc-snpstats r-cran-mockery r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-mass r-cran-testit r-cran-survival r-cran-pkgload r-cran-sp r-cran-sodium r-cran-lubridate r-cran-rmarkdown r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockr r-cran-waldo libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo libjs-jquery liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-titancna r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-foreach r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-iterators r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 180 newly installed, 0 to remove and 0 not upgraded. Need to get 184 MB of archives. After this operation, 518 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libasan6 amd64 10.2.1-6 [2065 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libatomic1 amd64 10.2.1-6 [9008 B] Get:17 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libitm1 amd64 10.2.1-6 [25.8 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 liblsan0 amd64 10.2.1-6 [828 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libtsan0 amd64 10.2.1-6 [2000 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libubsan1 amd64 10.2.1-6 [777 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libgcc-10-dev amd64 10.2.1-6 [2328 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libc-dev-bin amd64 2.31-13+deb11u10 [276 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 linux-libc-dev amd64 5.10.218-1 [1728 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libtirpc-dev amd64 1.3.1-1+deb11u1 [191 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libc6-dev amd64 2.31-13+deb11u10 [2362 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:34 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2+deb11u1 [156 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u12 [347 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u4 [1377 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:89 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 node-html5shiv all 3.7.3+dfsg-3 [12.9 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biobase amd64 2.50.0-1 [2229 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 r-bioc-s4vectors amd64 0.28.1-1 [2027 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 r-bioc-iranges amd64 2.24.1-1 [2202 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbi all 1.1.1-1 [619 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit amd64 4.0.4+dfsg-1 [422 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 r-cran-blob all 1.2.1-2 [49.1 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 r-cran-fastmap amd64 1.1.0-1 [64.7 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 r-cran-cachem amd64 1.0.3-1 [61.4 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 r-cran-memoise all 2.0.0-1 [52.9 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 r-cran-bh all 1.74.0-1 [5196 B] Get:112 http://deb.debian.org/debian bullseye/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 r-cran-rsqlite amd64 2.2.3-1 [1035 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 r-bioc-annotationdbi all 1.52.0-1 [4707 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 r-cran-generics all 0.1.0-1 [73.5 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 r-cran-purrr amd64 0.3.4-1+b1 [398 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyselect amd64 1.1.0+dfsg-1 [192 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 r-cran-dplyr amd64 1.0.4-1 [1143 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbplyr all 2.1.0-1 [802 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 r-cran-curl amd64 4.3+dfsg-1+b1 [151 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 r-cran-mime amd64 0.9-1+b1 [35.5 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 r-cran-sys amd64 3.4-1 [42.9 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 r-cran-openssl amd64 1.4.3+dfsg-2 [376 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 r-cran-httr all 1.4.2-1 [478 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocfilecache all 1.14.0+dfsg-1 [289 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 r-cran-formatr all 1.7-2 [151 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 r-cran-snow all 1:0.4.3-2 [109 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocparallel amd64 1.24.1-1 [1143 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml amd64 3.99-0.5-1 [1722 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 r-cran-hms all 1.0.0-1 [102 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.5.3-1 [729 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringr all 1.4.0-2 [199 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml2 amd64 1.3.2-1+b1 [270 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biomart all 2.46.2+dfsg-1 [414 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get:156 http://deb.debian.org/debian bullseye/main amd64 r-bioc-xvector amd64 0.30.0-1 [620 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biostrings amd64 2.58.0-1 [14.2 MB] Get:158 http://deb.debian.org/debian bullseye/main amd64 r-cran-bitops amd64 1.0-6-5 [23.6 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcurl amd64 1.98-1.2-1+b1 [787 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get:161 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicranges amd64 1.42.0+dfsg-1 [1856 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhtslib amd64 1.22.0+dfsg-1 [1024 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rsamtools amd64 2.6.0-1 [3659 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrixstats amd64 0.58.0-3 [664 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 r-bioc-delayedarray amd64 0.16.1+dfsg-1 [1798 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicalignments amd64 1.26.0-1 [2196 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rtracklayer amd64 1.50.0-1 [7467 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 r-bioc-bsgenome all 1.58.0-1 [7206 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicfeatures all 1.42.1+dfsg-1 [1834 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 r-bioc-variantannotation amd64 1.36.0-1 [3501 kB] Get:176 http://deb.debian.org/debian bullseye/main amd64 r-cran-codetools all 0.2-18-1 [91.8 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 r-cran-iterators all 1.0.13-1 [329 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 r-cran-foreach all 1.5.1-1 [120 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 r-cran-data.table amd64 1.13.6+dfsg-1 [1715 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 r-bioc-titancna amd64 1.28.0-2 [3951 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 184 MB in 5s (39.0 MB/s) Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6674 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../001-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../006-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../008-libpng16-16_1.6.37-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-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 .../010-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-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 .../012-libfontconfig1_2.13.1-4.2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-4.2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.13.1-4.2_amd64.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libasan6:amd64. Preparing to unpack .../014-libasan6_10.2.1-6_amd64.deb ... Unpacking libasan6:amd64 (10.2.1-6) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../015-libatomic1_10.2.1-6_amd64.deb ... Unpacking libatomic1:amd64 (10.2.1-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../016-libblas3_3.9.0-3+deb11u1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3+deb11u1) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../017-libgomp1_10.2.1-6_amd64.deb ... Unpacking libgomp1:amd64 (10.2.1-6) ... Selecting previously unselected package libitm1:amd64. Preparing to unpack .../018-libitm1_10.2.1-6_amd64.deb ... Unpacking libitm1:amd64 (10.2.1-6) ... Selecting previously unselected package liblsan0:amd64. Preparing to unpack .../019-liblsan0_10.2.1-6_amd64.deb ... Unpacking liblsan0:amd64 (10.2.1-6) ... Selecting previously unselected package libtsan0:amd64. 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Setting up node-html5shiv (3.7.3+dfsg-3) ... Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up linux-libc-dev:amd64 (5.10.218-1) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libasan6:amd64 (10.2.1-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up zip (3.0-12) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libtirpc-dev:amd64 (1.3.1-1+deb11u1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libpng16-16:amd64 (1.6.37-3) ... 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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 libtsan0:amd64 (10.2.1-6) ... Setting up libice6:amd64 (2:1.0.10-1) ... 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-render0:amd64 (1.14-3) ... Setting up libgcc-10-dev:amd64 (10.2.1-6) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libxcb-shm0: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 libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u12) ... Setting up libc6-dev:amd64 (2.31-13+deb11u10) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libstdc++-10-dev:amd64 (10.2.1-6) ... Setting up libboost1.74-dev:amd64 (1.74.0-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... 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 r-cran-bh (1.74.0-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... 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-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-formatr (1.7-2) ... Setting up r-cran-xml (3.99-0.5-1) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... 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 r-cran-rcpp (1.0.6-1) ... Setting up r-cran-curl (4.3+dfsg-1+b1) ... Setting up r-cran-codetools (0.2-18-1) ... 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-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... 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-mime (0.9-1+b1) ... Setting up r-cran-generics (0.1.0-1) ... Setting up r-cran-iterators (1.0.13-1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-xml2 (1.3.2-1+b1) ... Setting up r-cran-dbi (1.1.1-1) ... Setting up r-cran-foreach (1.5.1-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up r-cran-data.table (1.13.6+dfsg-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-bit (4.0.4+dfsg-1) ... 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-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-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-stringi (1.5.3-1) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-purrr (0.3.4-1+b1) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-cachem (1.0.3-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... 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-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-httr (1.4.2-1) ... Setting up r-cran-memoise (2.0.0-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... 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-biomart (2.46.2+dfsg-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Setting up r-bioc-rtracklayer (1.50.0-1) ... Setting up r-bioc-genomicfeatures (1.42.1+dfsg-1) ... Setting up r-bioc-bsgenome (1.58.0-1) ... Setting up r-bioc-variantannotation (1.36.0-1) ... Setting up r-bioc-titancna (1.28.0-2) ... Processing triggers for libc-bin (2.31-13+deb11u10) ... 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. 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m42.4s INFO: Running scripts post_install 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 0m42.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 0m44.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 0m44.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpds2qfkmn to testing 0m44.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m44.5s INFO: Running scripts pre_distupgrade 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_exceptions'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_exceptions'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 0m48.8s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8788 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 3s (4623 kB/s) Reading package lists... 0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 1m47.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-11-base libasan6 libgcc-10-dev libicu67 libldap-2.4-2 libstdc++-10-dev libtiff5 libtsan0 libwebp6 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1 The following NEW packages will be installed: gcc-11-base gcc-12-base libasan8 libcap2 libffi8 libfile-find-rule-perl libgcc-12-dev libgdbm-compat4 libgdbm6 libicu72 libldap-2.5-0 liblerc4 libnumber-compare-perl libperl5.36 libsemanage2 libsepol2 libssl3 libstdc++-12-dev libtext-glob-perl libtiff6 libtsan2 libwebp7 perl perl-modules-5.36 r-bioc-biocio r-bioc-keggrest r-cran-cpp11 r-cran-filelock r-cran-png r-cran-restfulr r-cran-rjson r-cran-yaml rpcsvc-proto usrmerge util-linux-extra The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libboost1.74-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcom-err2 libcrypt-dev libcrypt1 libcurl4 libdatrie1 libdb5.3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libnettle8 libnghttp2-14 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 libpcre2-8-0 libpcre3 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsmartcols1 libss2 libssh2-1 libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan0 libubsan1 libudev1 libunistring2 libuuid1 libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxcb1 libxext6 libxft2 libxml2 libxrender1 libxt6 libxxhash0 libzstd1 linux-libc-dev littler login logsave lsb-base mawk mount ncurses-base ncurses-bin node-html5shiv openssl passwd perl-base r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-titancna r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bit r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-foreach r-cran-formatr r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-iterators r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgkitten r-cran-purrr r-cran-r6 r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sed sensible-utils sysvinit-utils tar tzdata ucf unzip util-linux x11-common zip zlib1g zlib1g-dev 242 upgraded, 35 newly installed, 1 to remove and 0 not upgraded. Need to get 237 MB of archives. After this operation, 157 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u6 [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+deb12u7 [1899 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 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+deb12u7 [2758 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u7 [607 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 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+deb12u1 [147 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+deb12u1 [165 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+deb12u1 [107 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+deb12u1 [110 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+deb12u1 [1176 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2+deb12u1 [836 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B] Get:32 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b7 [1490 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+deb12u1 [94.3 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.26-1~deb12u2 [332 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.26-1~deb12u2 [108 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u3 [1405 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+deb12u1 [46.8 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B] Get:79 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:87 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:88 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 37~deb12u1 [13.3 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+deb12u1 [134 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+deb12u1 [28.6 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2024a-0+deb12u1 [297 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 gcc-11-base amd64 11.3.0-12 [38.4 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libasan6 amd64 11.3.0-12 [2050 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:122 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:148 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:174 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libtsan0 amd64 11.3.0-12 [2016 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:190 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:194 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:202 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:211 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:214 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-bioc-bsgenome all 1.66.3-1 [6997 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 r-bioc-variantannotation amd64 1.44.1-1 [3642 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 r-cran-data.table amd64 1.14.8+dfsg-1 [1683 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 r-bioc-titancna amd64 1.36.0-1 [3902 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 237 MB in 3s (88.7 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 35601 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u6_amd64.deb ... Unpacking base-files (12.4+deb12u6) over (11.1+deb11u10) ... Setting up base-files (12.4+deb12u6) ... 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 ... 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Preparing to unpack .../libc6_2.36-9+deb12u7_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u7) over (2.31-13+deb11u10) ... Setting up libc6:amd64 (2.36-9+deb12u7) ... (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 ... 35596 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u7_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u7) over (2.31-13+deb11u10) ... Setting up libc-bin (2.36-9+deb12u7) ... (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 ... 35681 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 ... 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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 ... 35685 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 ... 35685 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 ... 35693 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.26-1~deb12u2_amd64.deb ... Unpacking libsystemd0:amd64 (252.26-1~deb12u2) over (247.3-7+deb11u5) ... Setting up libsystemd0:amd64 (252.26-1~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 ... 35694 files and directories currently installed.) Preparing to unpack .../libudev1_252.26-1~deb12u2_amd64.deb ... Unpacking libudev1:amd64 (252.26-1~deb12u2) over (247.3-7+deb11u5) ... Setting up libudev1:amd64 (252.26-1~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 ... 35695 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 ... 35695 files and directories currently installed.) 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 ... 35698 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 ... 35698 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 ... 35698 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 ... 35698 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 ... 35698 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 ... 35700 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 ... 35705 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 ... 35705 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 ... 35705 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u3_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u3) over (3.7.1-5+deb11u5) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u3) ... (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 ... 35707 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 ... 35707 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 ... 35711 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 ... 35716 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 ... 35751 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 ... 35746 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 ... 35753 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 ... 35754 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 ... 35722 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 ... 35722 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 ... 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Setting up r-bioc-genomeinfodb (1.34.9-1) ... 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-dplyr (1.0.10-1) ... Setting up r-cran-dbplyr (2.3.0+dfsg-1) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-bioc-biocfilecache (2.6.1+dfsg-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-bioc-rsamtools (2.14.0-1) ... 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-biomart (2.54.0+dfsg-1) ... Setting up r-bioc-genomicalignments (1.34.0-1) ... Setting up r-bioc-rtracklayer (1.58.0-1) ... Setting up r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Setting up r-bioc-bsgenome (1.66.3-1) ... Setting up r-bioc-variantannotation (1.44.1-1) ... Setting up r-bioc-titancna (1.36.0-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for debianutils (5.7-0.5~deb12u1) ... 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. 1m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 1m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m48.3s DUMP: 913e17be84ed63a3110ce3137c1d003a - 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 1m48.5s DUMP: Package: r-bioc-titancna Version: 1.36.0-1 Installed-Size: 7613 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-biocgenerics (>= 0.31.6), r-bioc-iranges (>= 2.6.1), r-bioc-genomicranges (>= 1.24.3), r-bioc-variantannotation (>= 1.18.7), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.8.7), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description-en: Subclonal copy number and LOH prediction from whole genome sequencing Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Homepage: https://bioconductor.org/packages/TitanCNA/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.36.0-1_amd64.deb Size: 3901912 MD5sum: 456c00800dd8d518f7de2f64bfda5efe SHA256: 3e9ac90131fac6333087d97e6b560b6d54ce53c00f0744e04022f06d14ffb2d3 1m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 1m48.5s INFO: apt-cache knows about the following packages: r-bioc-titancna 1m48.5s INFO: Running scripts pre_install 1m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 1m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 1m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 1m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 1m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 1m48.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 1m48.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 1m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 1m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 1m48.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 1m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 1m48.7s DUMP: r-bioc-titancna: Installed: 1.36.0-1 Candidate: 1.36.0-1 Version table: *** 1.36.0-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 1m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 1m49.3s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-titancna is already the newest version (1.36.0-1). The following packages were automatically installed and are no longer required: gcc-11-base libasan6 libgcc-10-dev libicu67 libldap-2.4-2 libstdc++-10-dev libtiff5 libtsan0 libwebp6 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 1m49.3s INFO: Running scripts post_install 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 1m49.3s INFO: Running scripts post_distupgrade 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_exceptions'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_exceptions'] 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_zz_backports'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_zz_backports'] 1m49.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 1m51.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 1m51.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpds2qfkmn to sid 1m51.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m51.5s INFO: Running scripts pre_distupgrade 1m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_exceptions'] 1m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_exceptions'] 1m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 1m56.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9972 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7297 kB] Fetched 17.5 MB in 3s (5243 kB/s) Reading package lists... 1m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'update'] 1m56.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 3m42.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-11-base gcc-12-base libasan6 libgcc-10-dev libgcc-12-dev libicu67 libldap-2.4-2 libnsl-dev libperl5.36 libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libwebp6 perl-modules-5.36 r-bioc-biocfilecache r-bioc-biomart r-cran-assertthat r-cran-ellipsis r-cran-filelock r-cran-httr2 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost1.74-dev libcurl4 libdb5.3 libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libhogweed6 libnettle8 libpng16-16 libpsl5 libreadline8 libssh2-1 libssl3 libtirpc3 libxt6 The following NEW packages will be installed: fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax gcc-14-base javascript-common libapt-pkg6.0t64 libbibtex-parser-perl libboost1.83-dev libcurl4t64 libdb5.3t64 libext2fs2t64 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhogweed6t64 libhwasan0 libio-string-perl libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libkpathsea6 liblatex-tounicode-perl liblua5.4-0 libmpfi0 libmpfr6 libnettle8t64 libperl5.38t64 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libreadline8t64 libsharpyuv0 libssh2-1t64 libssl3t64 libstdc++-14-dev libsynctex2 libteckit0 libtexlua53-5 libtirpc3t64 libunistring5 libuv1t64 libxaw7 libxi6 libxmu6 libxpm4 libxt6t64 libyaml-0-2 libzzip-0-13t64 login.defs node-bootstrap-sass node-normalize.css pandoc pandoc-data perl-modules-5.38 r-bioc-biocstyle r-bioc-biocversion r-bioc-s4arrays r-bioc-sparsearray r-bioc-ucsc.utils r-cran-abind r-cran-base64enc r-cran-biocmanager r-cran-bookdown r-cran-bslib r-cran-commonmark r-cran-evaluate r-cran-fontawesome r-cran-fs r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr2 r-cran-jquerylib r-cran-knitr r-cran-later r-cran-promises r-cran-rmarkdown r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-tidyr r-cran-tinytex r-cran-xfun r-cran-xtable t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gcc-11-base gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libasan6 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcom-err2 libcrypt-dev libcrypt1 libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libnghttp2-14 libnsl-dev libnsl2 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 libpcre2-8-0 libpcre3 libpixman-1-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsm6 libsmartcols1 libss2 libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan0 libtsan2 libubsan1 libudev1 libuuid1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxft2 libxml2 libxrender1 libxss1 libxxhash0 libzstd1 linux-libc-dev littler login logsave mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base r-base-core 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-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-titancna r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-fansi r-cran-filelock r-cran-formatr r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgkitten r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common sed sensible-utils sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra x11-common zip zlib1g zlib1g-dev 245 upgraded, 109 newly installed, 18 to remove and 0 not upgraded. Need to get 421 MB of archives. After this operation, 713 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13.5 [72.8 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3+b2 [67.2 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.39-7 [1925 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.39-7 [51.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [189 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:9 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.1+dfsg-1 [178 kB] Get:10 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1+b1 [787 kB] Get:11 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.64.0-1 [2132 kB] Get:12 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-1 [1894 kB] Get:13 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:14 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:15 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.6+dfsg-1 [303 kB] Get:17 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.1-6 [1381 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.9.1-2 [463 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.39-7 [2791 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.39-7 [610 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.3.1-6 [2270 kB] Get:22 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:23 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1 [87.9 kB] Get:24 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get:25 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get:26 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:27 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-5 [2905 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-5 [4275 kB] Get:36 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-5 [236 kB] Get:37 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-5 [1643 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-7 [19.6 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 256.5-1 [381 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-2 [17.2 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-5 [89.8 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b4 [75.1 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Get:50 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.87 [119 kB] Get:51 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:52 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:53 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:69 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:70 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-1 [9652 B] Get:71 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:72 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:73 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:74 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:75 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:76 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:77 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:78 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-2 [46.0 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-2 [72.8 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-2 [714 kB] Get:81 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:82 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:83 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:84 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:85 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:86 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:87 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get:88 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:89 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:90 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.3.0-1 [502 kB] Get:91 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.16.0-1 [423 kB] Get:92 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1842 kB] Get:93 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-2 [837 kB] Get:96 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:97 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:98 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-0-3 [4127 kB] Get:99 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-2 [137 kB] Get:101 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:102 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:103 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:104 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-2 [25.9 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-2 [9288 B] Get:107 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-2 [2724 kB] Get:108 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-2 [1205 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-2 [1075 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.4.0-2 [2081 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-2 [145 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.4.0-2 [2431 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-2 [2461 kB] Get:114 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.4.0-2 [42.9 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-2 [1489 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-2 [2672 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-2 [2343 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:119 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-3.1 [10.6 MB] Get:120 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:121 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:122 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.2-2 [254 kB] Get:123 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:124 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:125 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:128 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:129 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:130 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.72.0-1 [6812 kB] Get:131 http://deb.debian.org/debian sid/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:132 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.36-1 [206 kB] Get:133 http://deb.debian.org/debian sid/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:134 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 0.24.0-1 [93.7 kB] Get:135 http://deb.debian.org/debian sid/main amd64 r-cran-xfun amd64 0.45+dfsg-1 [519 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:137 http://deb.debian.org/debian sid/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:138 http://deb.debian.org/debian sid/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:140 http://deb.debian.org/debian sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:143 http://deb.debian.org/debian sid/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:144 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.8-2 [107 kB] Get:145 http://deb.debian.org/debian sid/main amd64 r-cran-knitr all 1.47+dfsg-1 [912 kB] Get:146 http://deb.debian.org/debian sid/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.48.0-5 [148 kB] Get:148 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:149 http://deb.debian.org/debian sid/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:150 http://deb.debian.org/debian sid/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:151 http://deb.debian.org/debian sid/main amd64 javascript-common all 11+nmu1 [6260 B] Get:152 http://deb.debian.org/debian sid/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:154 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.0.8-1 [72.0 kB] Get:155 http://deb.debian.org/debian sid/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:156 http://deb.debian.org/debian sid/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:157 http://deb.debian.org/debian sid/main amd64 r-cran-tinytex all 0.51-1 [146 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:161 http://deb.debian.org/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:162 http://deb.debian.org/debian sid/main amd64 pandoc-data all 3.1.3-2 [445 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:164 http://deb.debian.org/debian sid/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:167 http://deb.debian.org/debian sid/main amd64 pandoc amd64 3.1.3+ds-3 [24.3 MB] Get:168 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:169 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-1 [16.0 kB] Get:170 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:171 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:172 http://deb.debian.org/debian sid/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:173 http://deb.debian.org/debian sid/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:174 http://deb.debian.org/debian sid/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:183 http://deb.debian.org/debian sid/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:185 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:186 http://deb.debian.org/debian sid/main amd64 r-cran-shiny all 1.8.1.1+dfsg-1 [2894 kB] Get:187 http://deb.debian.org/debian sid/main amd64 r-cran-rmarkdown all 2.27+dfsg-1 [1473 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libjs-lunr all 2.3.9~dfsg-2 [76.6 kB] Get:189 http://deb.debian.org/debian sid/main amd64 r-cran-bookdown all 0.40+dfsg-1 [1404 kB] Get:190 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:191 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:192 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.1-1 [28.3 MB] Get:193 http://deb.debian.org/debian sid/main amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [126 kB] Get:194 http://deb.debian.org/debian sid/main amd64 tex-common all 6.18 [32.5 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:196 http://deb.debian.org/debian sid/main amd64 liblatex-tounicode-perl all 0.54-2 [29.1 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libbibtex-parser-perl all 1.04+dfsg-1 [17.6 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [157 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [49.1 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [62.5 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [114 kB] Get:202 http://deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get:207 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.20 [89.5 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.50-3 [81.5 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.11.0-6 [843 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-7 [57.2 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-2 [186 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.8 [1045 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10-1 [303 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10-1 [334 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-2 [424 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.6-2 [1444 kB] Get:217 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.8 [1410 kB] Get:218 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:219 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:222 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-3 [59.4 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 256.5-1 [144 kB] Get:224 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:225 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.11 [1531 kB] Get:226 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.10-1 [32.7 kB] Get:227 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:228 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-7 [35.3 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:233 http://deb.debian.org/debian sid/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:238 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-7 [167 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-7 [199 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [35.0 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [219 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [48.0 kB] Get:243 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:244 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.81.1-3 [1496 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:251 http://deb.debian.org/debian sid/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8493 kB] Get:252 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:253 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:254 http://deb.debian.org/debian sid/main amd64 texlive-base all 2024.20240706-1 [22.7 MB] Get:255 http://deb.debian.org/debian sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:256 http://deb.debian.org/debian sid/main amd64 texlive-latex-base all 2024.20240706-1 [1274 kB] Get:257 http://deb.debian.org/debian sid/main amd64 texlive-bibtex-extra all 2024.20240706-2 [79.1 MB] Get:258 http://deb.debian.org/debian sid/main amd64 r-bioc-biocversion all 3.19.1-1 [10.9 kB] Get:259 http://deb.debian.org/debian sid/main amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [453 kB] Get:260 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [918 kB] Get:261 http://deb.debian.org/debian sid/main amd64 r-bioc-variantannotation amd64 1.50.0-1 [3508 kB] Get:262 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.15.4+dfsg-2.2 [1847 kB] Get:263 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:264 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:265 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:266 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-bioc-titancna amd64 1.42.0-1 [3911 kB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-httr2 all 1.0.2-1 [582 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.2-1 [507 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-tidyr amd64 1.3.1-1 [1163 kB] Get:273 http://deb.debian.org/debian sid/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get:274 http://deb.debian.org/debian sid/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:275 http://deb.debian.org/debian sid/main amd64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [301 kB] Get:276 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:277 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:278 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 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 2.60.1+dfsg-1 [452 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:282 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.50.0-1 [606 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amd64 util-linux amd64 2.40.2-7 [1217 kB] Get:329 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.40.2-7 [265 kB] Get:330 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.272 [10.0 kB] Get:331 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.4 [50.9 kB] Get:332 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-2 [32.4 kB] Get:333 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:334 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:335 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.7-1 [293 kB] Get:336 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b4 [90.1 kB] Get:337 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-4 [1232 kB] Get:338 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:339 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.43-8 [216 kB] Get:340 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:341 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1+b1 [47.3 kB] Get:342 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:343 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5-2 [270 kB] Get:344 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.1-1 [22.7 kB] Get:345 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.1-1 [210 kB] Get:346 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.1-1 [583 kB] Get:347 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-7 [154 kB] Get:348 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240622-2 [136 kB] Get:349 http://deb.debian.org/debian sid/main amd64 libasan6 amd64 11.5.0-1 [2046 kB] Get:350 http://deb.debian.org/debian sid/main amd64 libtsan0 amd64 11.5.0-1 [2018 kB] Get:351 http://deb.debian.org/debian sid/main amd64 gcc-11-base amd64 11.5.0-1 [42.1 kB] Get:352 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:353 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.1-1 [27.6 kB] Get:354 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-2 [152 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 421 MB in 4s (117 MB/s) (Reading database ... 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Unpacking perl-modules-5.38 (5.38.2-5) ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libsasl2-modules-db:amd64 depends on libdb5.3. libperl5.36:amd64 depends on libdb5.3. libpam-modules: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 ... 40562 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64:amd64. (Reading database ... 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Setting up perl-base (5.38.2-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41090 files and directories currently installed.) Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-7_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) over (2.1.28+dfsg-10) ... 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 ... 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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 ... 41089 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41088 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-7) ... Installing new version of config file /etc/security/namespace.init ... (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../01-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) over (3.0-13) ... Preparing to unpack .../02-libdeflate0_1.21-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.21-1) over (1.14-1) ... Preparing to unpack .../03-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) over (1:2.1.5-2) ... Preparing to unpack .../04-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) over (2024a-0+deb12u1) ... Preparing to unpack .../05-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) over (8.6.13+dfsg-2) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../06-libsharpyuv0_1.4.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... Preparing to unpack .../07-libwebp7_1.4.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1) over (1.2.4-0.2+deb12u1) ... Preparing to unpack .../08-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) over (2.1-6.1) ... Preparing to unpack .../09-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) over (4.0.0+ds-2) ... Preparing to unpack .../10-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) over (4.5.0-6+deb12u1) ... Preparing to unpack .../11-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) over (2.3.6-1) ... 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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 ... 62020 files and directories currently installed.) Removing libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:amd64. (Reading database ... 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Preparing to unpack .../libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) over (1.3.0-2) ... Preparing to unpack .../linux-libc-dev_6.10.4-1_all.deb ... Unpacking linux-libc-dev (6.10.4-1) over (6.1.94-1) ... Preparing to unpack .../bash_5.2.21-2.1+b1_amd64.deb ... Unpacking bash (5.2.21-2.1+b1) over (5.2.15-2+b7) ... Setting up bash (5.2.21-2.1+b1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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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 ... 63708 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_amd64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (Reading database ... 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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 ... 63708 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_amd64.deb ... Unpacking grep (3.11-4) over (3.8-5) ... Setting up grep (3.11-4) ... (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 ... 63708 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1.1_amd64.deb ... Unpacking gzip (1.12-1.1) over (1.12-1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1.1) ... (Reading database ... (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 ... 63708 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu2_amd64.deb ... Unpacking hostname (3.23+nmu2) over (3.23+nmu1) ... Setting up hostname (3.23+nmu2) ... Selecting previously unselected package login.defs. (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 ... 63708 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.16.0-4_all.deb ... Unpacking login.defs (1:4.16.0-4) ... Replacing files in old package login (1:4.13+dfsg1-1+b1) ... Setting up login.defs (1:4.16.0-4) ... Installing new version of config file /etc/login.defs ... (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 ... 63713 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-7_all.deb ... Unpacking libpam-runtime (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63712 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-7_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-7) over (1:4.13+dfsg1-1+b1) ... Setting up login (1:4.16.0-2+really2.40.2-7) ... Installing new version of config file /etc/pam.d/login ... (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 ... 63591 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-7_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-7) over (2.38.1-5+deb12u1) ... Setting up libsmartcols1:amd64 (2.40.2-7) ... (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 ... 63592 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-7_amd64.deb ... Unpacking util-linux (2.40.2-7) over (2.38.1-5+deb12u1) ... Setting up util-linux (2.40.2-7) ... (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 ... 63565 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.40.2-7_amd64.deb ... Adding 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-7) over (2.38.1-5+deb12u1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty Setting up util-linux-extra (2.40.2-7) ... (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 ... 63605 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.272_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.272) over (0.270) ... Setting up libdebconfclient0:amd64 (0.272) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63605 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.4_amd64.deb ... Unpacking base-passwd (3.6.4) over (3.6.1) ... Setting up base-passwd (3.6.4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63605 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-2_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-2) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63605 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-1_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:amd64 (1:2.5.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63605 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 ... 63605 files and directories currently installed.) Preparing to unpack .../libsepol2_3.7-1_amd64.deb ... Unpacking libsepol2:amd64 (3.7-1) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 63605 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b4_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b4) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.5-1+b4) ... (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 ... 63605 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.16.0-4_amd64.deb ... Unpacking passwd (1:4.16.0-4) over (1:4.13+dfsg1-1+b1) ... Setting up passwd (1:4.16.0-4) ... (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.1-1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.1-1) ... (Reading database ... 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Unpacking e2fsprogs (1.47.1-1) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../1-mount_2.40.2-7_amd64.deb ... Unpacking mount (2.40.2-7) over (2.38.1-5+deb12u1) ... Preparing to unpack .../2-mawk_1.3.4.20240622-2_amd64.deb ... Unpacking mawk (1.3.4.20240622-2) over (1.3.4.20200120-3.1) ... Preparing to unpack .../3-libasan6_11.5.0-1_amd64.deb ... Unpacking libasan6:amd64 (11.5.0-1) over (11.3.0-12) ... Preparing to unpack .../4-libtsan0_11.5.0-1_amd64.deb ... Unpacking libtsan0:amd64 (11.5.0-1) over (11.3.0-12) ... Preparing to unpack .../5-gcc-11-base_11.5.0-1_amd64.deb ... Unpacking gcc-11-base:amd64 (11.5.0-1) over (11.3.0-12) ... 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Setting up libglib2.0-0t64:amd64 (2.81.1-3) ... No schema files found: doing nothing. Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Setting up pandoc (3.1.3+ds-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgcc-12-dev:amd64 (12.4.0-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libc6-dev:amd64 (2.39-7) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libgcc-14-dev:amd64 (14.2.0-2) ... Setting up libstdc++-14-dev:amd64 (14.2.0-2) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.1) ... Setting up libcurl4t64:amd64 (8.9.1-2) ... Setting up libstdc++-12-dev:amd64 (12.4.0-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... 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Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up r-cran-commonmark (1.9.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Setting up texlive-base (2024.20240706-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up r-cran-filelock (1.0.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.12-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.4+dfsg-1) ... Setting up r-cran-rcpp (1.0.13-1) ... Setting up r-cran-curl (5.2.1+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.50.0-1) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.3.0-1) ... Setting up littler (0.3.20-1) ... Setting up r-bioc-matrixgenerics (1.16.0-1) ... Setting up r-cran-xfun (0.45+dfsg-1) ... Setting up r-cran-sys (3.4.2-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-abind (1.4-5-2) ... Setting up r-cran-digest (0.6.36-1) ... Setting up r-cran-yaml (2.3.8-2) ... Setting up r-cran-evaluate (0.24.0-1) ... Setting up r-cran-dbi (1.2.3-1) ... Setting up r-cran-highr (0.11+dfsg-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-data.table (1.15.4+dfsg-2.2) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-bioc-biocversion (3.19.1-1) ... Setting up r-cran-biocmanager (1.30.22+dfsg-2) ... Setting up r-bioc-zlibbioc (1.50.0+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 (2.64.0-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.3-1) ... Setting up texlive-latex-base (2024.20240706-1) ... Setting up r-cran-cpp11 (0.4.7-1) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-1) ... Setting up r-cran-later (1.3.2+dfsg-1) ... Setting up r-cran-matrix (1.7-0-3) ... Setting up r-cran-htmltools (0.5.8.1-1) ... Setting up r-cran-tinytex (0.51-1) ... Setting up r-cran-knitr (1.47+dfsg-1) ... Setting up r-cran-cachem (1.0.8-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up r-cran-xml2 (1.3.6-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up texlive-bibtex-extra (2024.20240706-2) ... Setting up r-cran-httr2 (1.0.2-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-promises (1.3.0+dfsg-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up r-cran-rsqlite (2.3.7-2) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-cran-shiny (1.8.1.1+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-cran-rmarkdown (2.27+dfsg-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-cran-dbplyr (2.4.0+dfsg-1) ... Setting up r-cran-bookdown (0.40+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up r-bioc-biocfilecache (2.12.0+dfsg-1) ... Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-bioc-keggrest (1.44.1+dfsg-1) ... Setting up r-bioc-annotationdbi (1.66.0-1) ... Setting up r-bioc-biomart (2.60.1+dfsg-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Setting up r-bioc-bsgenome (1.72.0-1) ... Setting up r-bioc-variantannotation (1.50.0-1) ... Setting up r-bioc-titancna (1.42.0-1) ... Processing triggers for libc-bin (2.39-7) ... Processing triggers for debianutils (5.20) ... 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 tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 3m42.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-yf', 'dist-upgrade'] 3m42.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m44.1s DUMP: b3c2e0013ae1ef221dd918ccbf9a3964 - 3m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 3m44.4s DUMP: Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description-en: Subclonal copy number and LOH prediction from whole genome sequencing Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Homepage: https://bioconductor.org/packages/TitanCNA/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b 3m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 3m44.4s INFO: apt-cache knows about the following packages: r-bioc-titancna 3m44.4s INFO: Running scripts pre_install 3m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 3m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 3m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 3m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 3m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 3m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 3m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 3m44.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 3m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 3m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 3m44.6s DUMP: r-bioc-titancna: Installed: 1.42.0-1 Candidate: 1.42.0-1 Version table: *** 1.42.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 3m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 3m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 3m45.3s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-titancna is already the newest version (1.42.0-1). The following packages were automatically installed and are no longer required: gcc-11-base gcc-12-base libasan6 libgcc-10-dev libgcc-12-dev libicu67 libldap-2.4-2 libnsl-dev libperl5.36 libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libwebp6 perl-modules-5.36 r-bioc-biocfilecache r-bioc-biomart r-cran-assertthat r-cran-ellipsis r-cran-filelock r-cran-httr2 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 3m45.3s INFO: Running scripts post_install 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 3m45.3s INFO: Running scripts post_distupgrade 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_exceptions'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_exceptions'] 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_zz_backports'] 3m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_distupgrade_zz_backports'] 3m45.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m48.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m48.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m51.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m51.6s INFO: Running scripts pre_install 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_database-server'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_exceptions'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_extras'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 3m51.6s 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: 3m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy'] 3m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 3m51.7s DUMP: r-bioc-titancna: Installed: 1.42.0-1 Candidate: 1.42.0-1 Version table: *** 1.42.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 3m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-cache', 'policy', 'r-bioc-titancna'] 3m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna=1.42.0-1'] 3m52.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-titancna is already the newest version (1.42.0-1). The following packages were automatically installed and are no longer required: gcc-11-base gcc-12-base libasan6 libgcc-10-dev libgcc-12-dev libicu67 libldap-2.4-2 libnsl-dev libperl5.36 libstdc++-10-dev libstdc++-12-dev libtiff5 libtirpc-dev libtsan0 libwebp6 perl-modules-5.36 r-bioc-biocfilecache r-bioc-biomart r-cran-assertthat r-cran-ellipsis r-cran-filelock r-cran-httr2 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', '-y', 'install', 'r-bioc-titancna=1.42.0-1'] 3m52.4s INFO: Running scripts post_install 3m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 3m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_install_exceptions'] 3m52.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m55.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 3m55.8s INFO: /lib converted to /usr/lib by /usr merge 3m55.8s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 4m0.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', '-ac', '--ignore-obsolete'] 4m6.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', '-ac', '--ignore-obsolete'] 4m6.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 4m6.7s DUMP: 0.15.6 4m6.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 4m6.7s INFO: Running adequate version 0.15.6 now. 4m6.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'r-bioc-titancna'] 4m6.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'r-bioc-titancna'] 4m6.9s INFO: Running scripts pre_remove 4m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 4m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 4m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 4m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 4m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 4m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 4m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 4m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 4m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 4m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 4m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_exceptions'] 4m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/pre_remove_exceptions'] 4m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 4m16.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.21-2.1+b1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed 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-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-lmodern fonts-lmodern 2.005-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-11-base:amd64 gcc-11-base 11.5.0-1 install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-2 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.43-8 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libasan6:amd64 libasan6 11.5.0-1 install ok installed libasan8:amd64 libasan8 14.2.0-2 install ok installed libatomic1:amd64 libatomic1 14.2.0-2 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libbibtex-parser-perl libbibtex-parser-perl 1.04+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-3.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.39-7 install ok installed libc-dev-bin libc-dev-bin 2.39-7 install ok installed libc6:amd64 libc6 2.39-7 install ok installed libc6-dev:amd64 libc6-dev 2.39-7 install ok installed libcairo2:amd64 libcairo2 1.18.0-3+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl4t64:amd64 libcurl4t64 8.9.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.21-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 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 libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b4 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-10-dev:amd64 libgcc-10-dev 10.2.1-6 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.4.0-2 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-2 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-2 deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.81.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 9.0.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-2 install ok installed libice6:amd64 libice6 2:1.0.10-1+b1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-5 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libitm1:amd64 libitm1 14.2.0-2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-4 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-es5-shim libjs-es5-shim 4.6.7-2 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-jquery-selectize.js libjs-jquery-selectize.js 0.12.6+dfsg-1.1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-json libjs-json 0~20221030+~1.0.8-1 install ok installed libjs-lunr libjs-lunr 2.3.9~dfsg-2 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libjs-microplugin.js libjs-microplugin.js 0.0.3+dfsg-1.1 install ok installed libjs-modernizr libjs-modernizr 3.13.0-0.1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-6 install ok installed libjs-prettify libjs-prettify 2015.12.04+dfsg-1.1 install ok installed libjs-sifter.js libjs-sifter.js 0.6.0+dfsg-3 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkpathsea6:amd64 libkpathsea6 2024.20240313.70630+ds-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblatex-tounicode-perl liblatex-tounicode-perl 0.54-2 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 2.5.18+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblsan0:amd64 liblsan0 14.2.0-2 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.6-3+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libmpfi0:amd64 libmpfi0 1.5.4+ds-3 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.62.1-2 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3+b2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29+b1 install ok installed libpaper1:amd64 libpaper1 1.1.29+b1 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 libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-5 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libpotrace0:amd64 libpotrace0 1.16-2+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libptexenc1:amd64 libptexenc1 2024.20240313.70630+ds-4 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-7 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b4 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.3.1-6 install ok installed libstdc++-10-dev:amd64 libstdc++-10-dev 10.2.1-6 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.4.0-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-2 install ok installed libsynctex2:amd64 libsynctex2 2024.20240313.70630+ds-4 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libteckit0:amd64 libteckit0 2.5.12+ds1-1 install ok installed libtexlua53-5:amd64 libtexlua53-5 2024.20240313.70630+ds-4 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+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtsan0:amd64 libtsan0 11.5.0-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-2 install ok installed libubsan1:amd64 libubsan1 14.2.0-2 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-5 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxaw7:amd64 libxaw7 2:1.0.14-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 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 libxml2:amd64 libxml2 2.12.7+dfsg-3+b1 install ok installed libxmu6:amd64 libxmu6 2:1.1.3-3+b2 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed libzzip-0-13t64:amd64 libzzip-0-13t64 0.13.72+dfsg.1-1.3 install ok installed linux-libc-dev linux-libc-dev 6.10.4-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed lsb-base lsb-base 11.6 install ok installed mawk mawk 1.3.4.20240622-2 install ok installed mount mount 2.40.2-7 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed node-bootstrap-sass node-bootstrap-sass 3.4.3-2 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openssl openssl 3.3.1-6 install ok installed pandoc pandoc 3.1.3+ds-3 install ok installed pandoc-data pandoc-data 3.1.3-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.38.2-5 install ok installed perl-base perl-base 5.38.2-5 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 5.38.2-5 install ok installed r-base-core r-base-core 4.4.1-1 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.66.0-1 install ok installed r-bioc-biobase r-bioc-biobase 2.64.0-1 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.12.0+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-1 install ok installed r-bioc-biocio r-bioc-biocio 1.14.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.38.0-2 install ok installed r-bioc-biocstyle r-bioc-biocstyle 2.32.1+dfsg-1 install ok installed r-bioc-biocversion r-bioc-biocversion 3.19.1-1 install ok installed r-bioc-biomart r-bioc-biomart 2.60.1+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.72.1+dfsg-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.72.0-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.30.1+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.40.1+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.12-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.40.0-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.56.0+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.56.1+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.38.1-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.44.1+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.16.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 3.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.20.0+dfsg-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.64.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.4.1+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.42.1+dfsg-1 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.4.8+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.34.0+dfsg-1 install ok installed r-bioc-titancna r-bioc-titancna 1.42.0-1 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.0.0+ds-2 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.50.0-1 install ok installed r-bioc-xvector r-bioc-xvector 0.44.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.50.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 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-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-biocmanager r-cran-biocmanager 1.30.22+dfsg-2 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-bookdown r-cran-bookdown 0.40+dfsg-1 install ok installed r-cran-bslib r-cran-bslib 0.7.0+dfsg-1 install ok installed r-cran-cachem r-cran-cachem 1.0.8-1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-commonmark r-cran-commonmark 1.9.1-1 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 5.2.1+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.15.4+dfsg-2.2 install ok installed r-cran-dbi r-cran-dbi 1.2.3-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.4.0+dfsg-1 install ok installed r-cran-digest r-cran-digest 0.6.36-1 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 0.24.0-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 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-fontawesome r-cran-fontawesome 0.5.2-1 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-formatr r-cran-formatr 1.14-2 install ok installed r-cran-fs r-cran-fs 1.6.4+dfsg-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-htmltools r-cran-htmltools 0.5.8.1-1 install ok installed r-cran-httpuv r-cran-httpuv 1.6.15+dfsg-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-httr2 r-cran-httr2 1.0.2-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-jquerylib r-cran-jquerylib 0.1.4+dfsg-4 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-knitr r-cran-knitr 1.47+dfsg-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-later r-cran-later 1.3.2+dfsg-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-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-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-matrix r-cran-matrix 1.7-0-3 install ok installed r-cran-matrixstats r-cran-matrixstats 1.3.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mime r-cran-mime 0.12-2 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-promises r-cran-promises 1.3.0+dfsg-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-rcpp r-cran-rcpp 1.0.13-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.14+dfsg-1+b1 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 1.1.4-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.27+dfsg-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.7-2 install ok installed r-cran-sass r-cran-sass 0.4.9+dfsg-1 install ok installed r-cran-shiny r-cran-shiny 1.8.1.1+dfsg-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-sourcetools r-cran-sourcetools 0.1.7-1-1 install ok installed r-cran-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-sys r-cran-sys 3.4.2-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-tinytex r-cran-tinytex 0.51-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed r-cran-xfun r-cran-xfun 0.45+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.17-1 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 2.3.8-2 install ok installed readline-common readline-common 8.2-4 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed t1utils t1utils 1.41-4 install ok installed tar tar 1.35+dfsg-3 install ok installed tex-common tex-common 6.18 install ok installed texlive-base texlive-base 2024.20240706-1 install ok installed texlive-bibtex-extra texlive-bibtex-extra 2024.20240706-2 install ok installed texlive-binaries texlive-binaries 2024.20240313.70630+ds-4 install ok installed texlive-latex-base texlive-latex-base 2024.20240706-1 install ok installed tzdata tzdata 2024a-4 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 2.40.2-7 install ok installed util-linux-extra util-linux-extra 2.40.2-7 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1 4m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 4m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'gcc-11-base:amd64', 'javascript-common', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libkpathsea6:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-titancna'] 4m21.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Package 'libglib2.0-0' 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: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax gcc-11-base javascript-common libasan6 libasan8 libatomic1 libbibtex-parser-perl libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-14-dev libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu67 libicu72 libio-string-perl libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libkpathsea6 liblapack3 liblatex-tounicode-perl libldap-2.4-2 libldap-2.5-0 liblerc4 liblsan0 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-10-dev libstdc++-12-dev libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff5 libtiff6 libtirpc-dev libtk8.6 libtsan0 libtsan2 libubsan1 libuv1t64 libwebp6 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-titancna r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-foreach r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-httr2 r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 283 to remove and 0 not upgraded. After this operation, 1277 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 ... 63639 files and directories currently installed.) Removing r-bioc-titancna (1.42.0-1) ... Removing r-bioc-variantannotation (1.50.0-1) ... Removing r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Removing r-bioc-bsgenome (1.72.0-1) ... Removing r-bioc-biocstyle (2.32.1+dfsg-1) ... Removing r-cran-bookdown (0.40+dfsg-1) ... Removing r-cran-rmarkdown (2.27+dfsg-1) ... Removing r-cran-shiny (1.8.1.1+dfsg-1) ... Removing texlive-bibtex-extra (2024.20240706-2) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-knitr (1.47+dfsg-1) ... Removing libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing texlive-latex-base (2024.20240706-1) ... Removing fonts-lmodern (2.005-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing libstdc++-10-dev:amd64 (10.2.1-6) ... Removing libgcc-10-dev:amd64 (10.2.1-6) ... Removing libtsan0:amd64 (11.5.0-1) ... Removing libasan6:amd64 (11.5.0-1) ... Removing gcc-11-base:amd64 (11.5.0-1) ... Removing r-cran-bslib (0.7.0+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (11+nmu1) ... Removing libstdc++-12-dev:amd64 (12.4.0-2) ... Removing libgcc-12-dev:amd64 (12.4.0-2) ... Removing texlive-base (2024.20240706-1) ... Removing libbibtex-parser-perl (1.04+dfsg-1) ... Removing r-bioc-biomart (2.60.1+dfsg-1) ... Removing r-cran-httr2 (1.0.2-1) ... Removing r-bioc-annotationdbi (1.66.0-1) ... Removing r-bioc-keggrest (1.44.1+dfsg-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing r-cran-data.table (1.15.4+dfsg-2.2) ... Removing libicu67:amd64 (67.1-7) ... Removing r-bioc-biocfilecache (2.12.0+dfsg-1) ... Removing r-cran-dbplyr (2.4.0+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... 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 libio-string-perl (1.08-4) ... Removing libjs-d3 (3.5.17-4) ... Removing libjs-es5-shim (4.6.7-2) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-highlight.js (9.18.5+dfsg1-2) ... Removing r-cran-jquerylib (0.1.4+dfsg-4) ... Removing libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Removing libjs-jquery-datatables (1.11.5+dfsg-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-json (0~20221030+~1.0.8-1) ... Removing libjs-lunr (2.3.9~dfsg-2) ... Removing libjs-microplugin.js (0.0.3+dfsg-1.1) ... Removing libjs-modernizr (3.13.0-0.1) ... Removing libjs-prettify (2015.12.04+dfsg-1.1) ... Removing libjs-sifter.js (0.6.0+dfsg-3) ... Removing liblatex-tounicode-perl (0.54-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing pandoc (3.1.3+ds-3) ... Removing liblua5.4-0:amd64 (5.4.6-3+b1) ... Removing libnsl-dev:amd64 (1.3.0-3+b2) ... Removing r-cran-png (0.1-8-1+b1) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Removing r-cran-httpuv (1.6.15+dfsg-1) ... Removing r-cran-sass (0.4.9+dfsg-1) ... Removing r-cran-fs (1.6.4+dfsg-1) ... Removing libuv1t64:amd64 (1.48.0-5) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libyaml-0-2:amd64 (0.2.5-1+b1) ... Removing littler (0.3.20-1) ... Removing node-bootstrap-sass (3.4.3-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing pandoc-data (3.1.3-2) ... Removing r-bioc-biocversion (3.19.1-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-fontawesome (0.5.2-1) ... Removing r-cran-htmltools (0.5.8.1-1) ... Removing r-cran-base64enc (0.1-3-3) ... Removing r-cran-biocmanager (1.30.22+dfsg-2) ... Removing r-cran-rsqlite (2.3.7-2) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.8-1) ... Removing r-cran-dplyr (1.1.4-1) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-foreach (1.5.2-1) ... Removing r-cran-commonmark (1.9.1-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-dbi (1.2.3-1) ... Removing r-cran-digest (0.6.36-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (0.24.0-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sourcetools (0.1.7-1-1) ... Removing r-cran-tinytex (0.51-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing r-cran-xfun (0.45+dfsg-1) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-bioc-rtracklayer (1.64.0-1) ... Removing r-bioc-genomicalignments (1.40.0-1) ... Removing r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Removing r-bioc-delayedarray (0.30.1+dfsg-1) ... Removing r-bioc-sparsearray (1.4.8+dfsg-1) ... Removing r-bioc-s4arrays (1.4.1+dfsg-1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-bioc-rsamtools (2.20.0+dfsg-1) ... Removing r-bioc-biocparallel (1.38.0-2) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-promises (1.3.0+dfsg-1) ... Removing texlive-binaries (2024.20240313.70630+ds-4) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-3.1) ... Removing libstdc++-14-dev:amd64 (14.2.0-2) ... Removing libgcc-14-dev:amd64 (14.2.0-2) ... Removing libasan8:amd64 (14.2.0-2) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing r-bioc-genomicranges (1.56.1+dfsg-1) ... Removing r-bioc-xvector (0.44.0-1) ... Removing r-bioc-rhtslib (3.0.0+dfsg-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Removing libc6-dev:amd64 (2.39-7) ... Removing libc-dev-bin (2.39-7) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libhwasan0:amd64 (14.2.0-2) ... Removing libxaw7:amd64 (2:1.0.14-1+b2) ... Removing libxmu6:amd64 (2:1.1.3-3+b2) ... Removing libitm1:amd64 (14.2.0-2) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Removing libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Removing liblsan0:amd64 (14.2.0-2) ... Removing libmpfi0:amd64 (1.5.4+ds-3) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libpotrace0:amd64 (1.16-2+b1) ... Removing libquadmath0:amd64 (14.2.0-2) ... Removing libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Removing libteckit0:amd64 (2.5.12+ds1-1) ... Removing libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Removing libtsan2:amd64 (14.2.0-2) ... Removing libubsan1:amd64 (14.2.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxpm4:amd64 (1:3.5.17-1+b1) ... Removing libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Removing linux-libc-dev (6.10.4-1) ... Removing r-bioc-biobase (2.64.0-1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Removing r-bioc-ucsc.utils (1.0.0+ds-2) ... Removing r-bioc-iranges (2.38.1-1) ... Removing r-bioc-matrixgenerics (1.16.0-1) ... Removing r-bioc-biocio (1.14.0+dfsg-1) ... Removing r-bioc-genomeinfodbdata (1.2.12-1) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... 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-vctrs (0.6.5-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-cpp11 (0.4.7-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-2) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-later (1.3.2+dfsg-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-matrixstats (1.3.0-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-sys (3.4.2-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing r-cran-yaml (2.3.8-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing tex-common (6.18) ... Removing t1utils (1.41-4) ... Removing r-cran-matrix (1.7-0-3) ... Removing r-cran-rcpp (1.0.13-1) ... Removing r-cran-curl (5.2.1+dfsg-1) ... Removing libxml2:amd64 (2.12.7+dfsg-3+b1) ... Removing r-bioc-s4vectors (0.42.1+dfsg-1) ... Removing r-bioc-biocgenerics (0.50.0-1) ... Removing r-cran-cli (3.6.2-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-base-core (4.4.1-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Removing libpango-1.0-0:amd64 (1.54.0+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 libharfbuzz0b:amd64 (9.0.0-1) ... Removing libglib2.0-0t64:amd64 (2.81.1-3) ... Removing libatomic1:amd64 (14.2.0-2) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libcairo2:amd64 (1.18.0-3+b1) ... Removing libcurl4t64:amd64 (8.9.1-2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.21-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgfortran5:amd64 (14.2.0-2) ... Removing libgomp1:amd64 (14.2.0-2) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libsm6:amd64 (2:1.2.3-1+b1) ... Removing libice6:amd64 (2:1.0.10-1+b1) ... Removing libicu72:amd64 (72.1-5) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.62.1-2) ... Removing libpaper-utils (1.1.29+b1) ... Removing libpaper1:amd64 (1.1.29+b1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... 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+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-7) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) ... Removing libwebp7:amd64 (1.4.0-0.1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libxss1:amd64 (1:1.2.3-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing openssl (3.3.1-6) ... Removing readline-common (8.2-4) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing 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 libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Processing triggers for libc-bin (2.39-7) ... 4m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'gcc-11-base:amd64', 'javascript-common', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libkpathsea6:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-titancna'] 4m21.5s INFO: Running scripts post_remove 4m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_remove_exceptions'] 4m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_remove_exceptions'] 4m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'gcc-11-base:amd64', 'javascript-common', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libkpathsea6:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 4m22.2s DUMP: (Reading database ... 9432 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. 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 Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-glyphicons-halflings which isn't installed Purging configuration files for fonts-lmodern (2.005-1) ... dpkg: warning: while removing fonts-lmodern, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-mathjax which isn't installed dpkg: warning: ignoring request to remove gcc-11-base which isn't installed Purging configuration files for javascript-common (11+nmu1) ... 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 libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbibtex-parser-perl 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 libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 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 Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... 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 libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 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-14-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.81.1-3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhwasan0 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-string-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 libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed Purging configuration files for libjs-bootstrap4 (4.6.1+dfsg1-4) ... dpkg: warning: ignoring request to remove libjs-d3 which isn't installed dpkg: warning: ignoring request to remove libjs-es5-shim which isn't installed dpkg: warning: ignoring request to remove libjs-highlight.js 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-jquery-datatables which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-selectize.js which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-json which isn't installed dpkg: warning: ignoring request to remove libjs-lunr which isn't installed dpkg: warning: ignoring request to remove libjs-mathjax which isn't installed dpkg: warning: ignoring request to remove libjs-microplugin.js which isn't installed dpkg: warning: ignoring request to remove libjs-modernizr which isn't installed Purging configuration files for libjs-popper.js (1.16.1+ds-6) ... dpkg: warning: ignoring request to remove libjs-prettify which isn't installed dpkg: warning: ignoring request to remove libjs-sifter.js which isn't installed dpkg: warning: ignoring request to remove libjs-twitter-bootstrap-datepicker which isn't installed dpkg: warning: ignoring request to remove libkpathsea6 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblatex-tounicode-perl 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 liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblua5.4-0 which isn't installed dpkg: warning: ignoring request to remove libmpfi0 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 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 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+b1) ... 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 libpotrace0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libptexenc1 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 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 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 libssh2-1t64 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++-14-dev which isn't installed dpkg: warning: ignoring request to remove libsynctex2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libteckit0 which isn't installed dpkg: warning: ignoring request to remove libtexlua53-5 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 libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtk8.6 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 libuv1t64 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 libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxaw7 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 libxcb1 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 libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmu6 which isn't installed dpkg: warning: ignoring request to remove libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrender1 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 libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove libzzip-0-13t64 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 dpkg: warning: ignoring request to remove node-bootstrap-sass which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove node-normalize.css which isn't installed Purging configuration files for openssl (3.3.1-6) ... dpkg: warning: ignoring request to remove pandoc which isn't installed dpkg: warning: ignoring request to remove pandoc-data which isn't installed Purging configuration files for r-base-core (4.4.1-1) ... 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-biocstyle which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocversion 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-bsgenome 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-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-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-keggrest which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-variantannotation which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-base64enc which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-biocmanager 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-bookdown which isn't installed dpkg: warning: ignoring request to remove r-cran-bslib which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli 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-commonmark 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-data.table which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-dbplyr 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-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-fontawesome which isn't installed dpkg: warning: ignoring request to remove r-cran-foreach which isn't installed dpkg: warning: ignoring request to remove r-cran-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-generics 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-highr which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-htmltools which isn't installed dpkg: warning: ignoring request to remove r-cran-httpuv which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-httr2 which isn't installed dpkg: warning: ignoring request to remove r-cran-iterators which isn't installed dpkg: warning: ignoring request to remove r-cran-jquerylib which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-knitr which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-later which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-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-magrittr 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-mime 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-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-plogr 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-prettyunits 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-promises 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-rcpp 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-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-rmarkdown 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-sass which isn't installed dpkg: warning: ignoring request to remove r-cran-shiny which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-sourcetools which isn't installed dpkg: warning: ignoring request to remove r-cran-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-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-tinytex 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-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xfun which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-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 rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove t1utils which isn't installed Purging configuration files for tex-common (6.18) ... Purging configuration files for texlive-base (2024.20240706-1) ... Purging configuration files for texlive-bibtex-extra (2024.20240706-2) ... dpkg: warning: ignoring request to remove texlive-binaries which isn't installed Purging configuration files for texlive-latex-base (2024.20240706-1) ... 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+23.1) ... 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 4m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'gcc-11-base:amd64', 'javascript-common', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libkpathsea6:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 4m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', 'r-bioc-titancna'] 4m22.2s DUMP: dpkg: warning: ignoring request to remove r-bioc-titancna which isn't installed 4m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', 'r-bioc-titancna'] 4m22.2s INFO: Running scripts post_purge 4m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_purge_exceptions'] 4m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_purge_exceptions'] 4m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', '--pending'] 4m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--purge', '--pending'] 4m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--remove', '--pending'] 4m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg', '--remove', '--pending'] 4m22.3s INFO: Running scripts post_test 4m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_test_exceptions'] 4m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'tmp/scripts/post_test_exceptions'] 4m22.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 4m23.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 4m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-divert', '--list'] 4m23.0s DUMP: diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files diversion of /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 diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra 4m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'dpkg-divert', '--list'] 4m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'clean'] 4m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn', 'apt-get', 'clean'] 4m23.2s DEBUG: Recording chroot state 4m24.1s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fonts-lmodern, fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fonts-lmodern, 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-font-awesome, fonts-glyphicons-halflings, fonts-mathjax, fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-font-awesome, fonts-glyphicons-halflings, fonts-dejavu-mono, fonts-dejavu-core /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 4m24.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/shm'] 4m24.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/shm'] 4m24.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/console'] 4m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/console'] 4m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/ptmx'] 4m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/ptmx'] 4m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts'] 4m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/dev/pts'] 4m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/proc'] 4m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn/proc'] 4m24.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 4m25.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpds2qfkmn'] 4m25.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpds2qfkmn 4m25.2s INFO: PASS: Upgrading between Debian distributions. 4m25.2s INFO: PASS: All tests. 4m25.2s INFO: piuparts run ends. ret=0 End: 2024-08-18 20:42:25 GMT