Start: 2024-03-05 11:44:35 GMT [stable] Package: r-bioc-purecn Version: 1.20.0+dfsg-3 Installed-Size: 8174 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-bioc-rhdf5, r-cran-matrix Recommends: r-cran-testthat Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-rmarkdown Description: copy number calling and SNV classification using targeted short read sequencing Homepage: https://bioconductor.org/packages/PureCN/ Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_1.20.0+dfsg-3_all.deb Size: 5304444 MD5sum: 2b0c26ac57680bd3e5885fcbb16d7a32 SHA256: 675a310b8cda855c6b19a4efe05cb04cf899df0cfc833fbed1775a5a90af3dfd [testing] Package: r-bioc-purecn Version: 2.4.0+dfsg-1 Installed-Size: 6925 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biobase, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-cran-mclust, r-bioc-rhdf5, r-cran-matrix Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-r.utils, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-markdown, r-cran-rmarkdown, r-cran-testthat Description: copy number calling and SNV classification using targeted short read sequencing Homepage: https://bioconductor.org/packages/PureCN/ Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_2.4.0+dfsg-1_all.deb Size: 6025432 MD5sum: 63310446847d2c1ec0b260bf4a1f8c41 SHA256: 6fca9f573ba611b541592defbfa086a288b8b048dbddd6652560a56050a14dca [sid] Package: r-bioc-purecn Version: 2.8.1+dfsg-1 Installed-Size: 6916 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biobase, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-cran-mclust, r-bioc-rhdf5, r-cran-matrix Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-r.utils, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-markdown, r-cran-rmarkdown, r-cran-testthat Description: copy number calling and SNV classification using targeted short read sequencing Homepage: https://bioconductor.org/packages/PureCN/ Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_2.8.1+dfsg-1_all.deb Size: 6014792 MD5sum: 6b7c7e0737b43e56d12dff8140d3cb1e SHA256: a9b3c22616d7d02647cea2819e03e91b8b661c0630be685f414889594a60ec24 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-purecn=2.8.1+dfsg-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 1.3.1~202401311836~1.3-2-g28295102 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-purecn=2.8.1+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpwrw8viat 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpwrw8viat 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', '--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/tmpwrw8viat', '--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/tmpwrw8viat/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/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/tmpwrw8viat/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/tmpwrw8viat/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/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/tmpwrw8viat/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 0m1.4s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.1s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.1s INFO: Running scripts post_setup 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', '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/tmpwrw8viat', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s 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/tmpwrw8viat'] 0m3.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 0m3.8s INFO: Running scripts is_testable 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/is_testable_uninstallable'] 0m3.9s INFO: Running scripts pre_test 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_test_exceptions'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_test_root_password'] 0m3.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_test_root_password'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m4.1s DUMP: Package: r-bioc-purecn Version: 1.20.0+dfsg-3 Installed-Size: 8174 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-bioc-rhdf5, r-cran-matrix Recommends: r-cran-testthat Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-rmarkdown Description-en: copy number calling and SNV classification using targeted short read sequencing This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples. Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Homepage: https://bioconductor.org/packages/PureCN/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_1.20.0+dfsg-3_all.deb Size: 5304444 MD5sum: 2b0c26ac57680bd3e5885fcbb16d7a32 SHA256: 675a310b8cda855c6b19a4efe05cb04cf899df0cfc833fbed1775a5a90af3dfd 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m4.1s INFO: apt-cache knows about the following packages: r-bioc-purecn 0m4.1s INFO: Running scripts pre_install 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 0m4.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m4.3s DUMP: r-bioc-purecn: Installed: (none) Candidate: 1.20.0+dfsg-3 Version table: 1.20.0+dfsg-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m46.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core hdf5-helpers libaec-dev libaec0 libasan6 libatomic1 libblas3 libblosc1 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 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice6 libicu67 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev 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 libsnappy1v5 libssh2-1 libstdc++-10-dev libsz2 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-dnacopy r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib 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-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-hms r-cran-httr r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo 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 libhdf5-doc 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-foreach r-cran-bbmisc r-bioc-shortread r-cran-codetools 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-cran-pscbs r-cran-covr r-cran-optparse r-cran-tinytest r-bioc-limma r-cran-roxygen2 r-cran-htmlwidgets r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg r-cran-viridis r-cran-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-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-forcats r-cran-lubridate r-cran-httpuv r-cran-readr r-cran-magick r-cran-plyr r-cran-getopt r-cran-base64enc r-cran-cpp11 r-cran-inline r-cran-gh r-cran-rvest r-cran-dichromat r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-mockery r-cran-usethis r-cran-formattable r-cran-htmltools r-cran-tidyr r-cran-zeallot 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-batchjobs r-cran-doparallel r-cran-batchtools r-cran-rmpi r-bioc-biovizbase r-bioc-shortread r-bioc-annotate r-cran-knitr r-cran-rmarkdown r-bioc-biocstyle r-bioc-snpstats r-cran-cliapp r-cran-mockery r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-testit r-cran-codetools r-cran-survival r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-sodium r-cran-lubridate r-cran-mockr r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets 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 hdf5-helpers libaec-dev libaec0 libasan6 libatomic1 libblas3 libblosc1 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 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice6 libicu67 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev 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 libsnappy1v5 libssh2-1 libstdc++-10-dev libsz2 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-dnacopy r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-purecn r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib 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-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-hms r-cran-httr r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 226 newly installed, 0 to remove and 0 not upgraded. Need to get 219 MB of archives. After this operation, 580 MB of additional disk space will be used. 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http://deb.debian.org/debian bullseye/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 libtirpc-dev amd64 1.3.1-1+deb11u1 [191 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libc6-dev amd64 2.31-13+deb11u8 [2361 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:40 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libhdf5-cpp-103-1 amd64 1.10.6+repack-4+deb11u1 [141 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libhdf5-fortran-102 amd64 1.10.6+repack-4+deb11u1 [105 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-fortran-100 amd64 1.10.6+repack-4+deb11u1 [56.8 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-cpp-100 amd64 1.10.6+repack-4+deb11u1 [37.7 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libhdf5-dev amd64 1.10.6+repack-4+deb11u1 [2438 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:105 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 node-html5shiv all 3.7.3+dfsg-3 [12.9 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biobase amd64 2.50.0-1 [2229 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 r-bioc-s4vectors amd64 0.28.1-1 [2027 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 r-bioc-iranges amd64 2.24.1-1 [2202 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbi all 1.1.1-1 [619 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit amd64 4.0.4+dfsg-1 [422 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 r-cran-blob all 1.2.1-2 [49.1 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 r-cran-fastmap amd64 1.1.0-1 [64.7 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 r-cran-cachem amd64 1.0.3-1 [61.4 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 r-cran-memoise all 2.0.0-1 [52.9 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 r-cran-bh all 1.74.0-1 [5196 B] Get:128 http://deb.debian.org/debian bullseye/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 r-cran-rsqlite amd64 2.2.3-1 [1035 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 r-bioc-annotationdbi all 1.52.0-1 [4707 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 r-cran-generics all 0.1.0-1 [73.5 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 r-cran-purrr amd64 0.3.4-1+b1 [398 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyselect amd64 1.1.0+dfsg-1 [192 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 r-cran-dplyr amd64 1.0.4-1 [1143 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbplyr all 2.1.0-1 [802 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 r-cran-curl amd64 4.3+dfsg-1+b1 [151 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 r-cran-mime amd64 0.9-1+b1 [35.5 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 r-cran-sys amd64 3.4-1 [42.9 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 r-cran-openssl amd64 1.4.3+dfsg-2 [376 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 r-cran-httr all 1.4.2-1 [478 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocfilecache all 1.14.0+dfsg-1 [289 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 r-cran-formatr all 1.7-2 [151 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 r-cran-snow all 1:0.4.3-2 [109 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocparallel amd64 1.24.1-1 [1143 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml amd64 3.99-0.5-1 [1722 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 r-cran-hms all 1.0.0-1 [102 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.5.3-1 [729 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringr all 1.4.0-2 [199 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml2 amd64 1.3.2-1+b1 [270 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biomart all 2.46.2+dfsg-1 [414 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get:171 http://deb.debian.org/debian bullseye/main amd64 r-bioc-xvector amd64 0.30.0-1 [620 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biostrings amd64 2.58.0-1 [14.2 MB] Get:173 http://deb.debian.org/debian bullseye/main amd64 r-cran-bitops amd64 1.0-6-5 [23.6 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcurl amd64 1.98-1.2-1+b1 [787 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get:176 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicranges amd64 1.42.0+dfsg-1 [1856 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhtslib amd64 1.22.0+dfsg-1 [1024 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rsamtools amd64 2.6.0-1 [3659 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrixstats amd64 0.58.0-3 [664 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 r-bioc-delayedarray amd64 0.16.1+dfsg-1 [1798 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicalignments amd64 1.26.0-1 [2196 kB] Get:187 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rtracklayer amd64 1.50.0-1 [7467 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 r-bioc-bsgenome all 1.58.0-1 [7206 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 r-bioc-dnacopy amd64 1.64.0-1 [420 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicfeatures all 1.42.1+dfsg-1 [1834 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 r-bioc-variantannotation amd64 1.36.0-1 [3501 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 r-cran-data.table amd64 1.13.6+dfsg-1 [1715 kB] Get:194 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:195 http://deb.debian.org/debian bullseye/main amd64 r-cran-brio amd64 1.1.1-1 [31.7 kB] Get:196 http://deb.debian.org/debian bullseye/main amd64 r-cran-ps amd64 1.5.0-1 [277 kB] Get:197 http://deb.debian.org/debian bullseye/main amd64 r-cran-processx amd64 3.4.5-1 [295 kB] Get:198 http://deb.debian.org/debian bullseye/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:199 http://deb.debian.org/debian bullseye/main amd64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:200 http://deb.debian.org/debian bullseye/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:201 http://deb.debian.org/debian bullseye/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:202 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:203 http://deb.debian.org/debian bullseye/main amd64 r-cran-rstudioapi all 0.13-1 [262 kB] Get:204 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:205 http://deb.debian.org/debian bullseye/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:206 http://deb.debian.org/debian bullseye/main amd64 r-cran-diffobj amd64 0.3.2-1 [1069 kB] Get:207 http://deb.debian.org/debian bullseye/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:208 http://deb.debian.org/debian bullseye/main amd64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get:209 http://deb.debian.org/debian bullseye/main amd64 r-cran-testthat amd64 3.0.1-1 [1451 kB] Get:210 http://deb.debian.org/debian bullseye/main amd64 r-cran-isoband amd64 0.2.3-2 [2085 kB] Get:211 http://deb.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-53.1-1 [1115 kB] Get:212 http://deb.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.152-1 [2241 kB] Get:213 http://deb.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-34-1 [2998 kB] Get:214 http://deb.debian.org/debian bullseye/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:215 http://deb.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:216 http://deb.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 2.0-0+dfsg-1 [1684 kB] Get:217 http://deb.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:218 http://deb.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:219 http://deb.debian.org/debian bullseye/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:220 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get:221 http://deb.debian.org/debian bullseye/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:222 http://deb.debian.org/debian bullseye/main amd64 r-cran-vgam amd64 1.1-5-1 [6977 kB] Get:223 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhdf5lib amd64 1.12.1+dfsg-3+b1 [27.9 kB] Get:224 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhdf5filters amd64 1.2.0+dfsg2-1 [22.1 kB] Get:225 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhdf5 amd64 2.34.0+dfsg-1 [548 kB] Get:226 http://deb.debian.org/debian bullseye/main amd64 r-bioc-purecn all 1.20.0+dfsg-3 [5304 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 219 MB in 7s (33.4 MB/s) 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Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-httr (1.4.2-1) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-memoise (2.0.0-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-tidyselect (1.1.0+dfsg-1) ... Setting up r-cran-hms (1.0.0-1) ... Setting up r-cran-blob (1.2.1-2) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-cran-dplyr (1.0.4-1) ... Setting up r-cran-dbplyr (2.1.0-1) ... Setting up r-cran-rsqlite (2.2.3-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-bioc-biocfilecache (1.14.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.52.0-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-waldo (0.2.3-2) ... 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-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-bioc-bsgenome (1.58.0-1) ... Setting up r-bioc-variantannotation (1.36.0-1) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up r-bioc-purecn (1.20.0+dfsg-3) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m46.6s INFO: Running scripts post_install 0m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 0m46.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 0m47.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 0m47.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpwrw8viat to testing 0m47.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m47.8s INFO: Running scripts pre_distupgrade 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_exceptions'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_exceptions'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m47.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m47.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 0m51.3s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8786 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 3s (5957 kB/s) Reading package lists... 0m51.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 0m51.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 1m56.2s 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 libcurl4-openssl-dev libffi8 libfile-find-rule-perl libgcc-12-dev libgdbm-compat4 libgdbm6 libicu72 libldap-2.5-0 liblerc4 libnumber-compare-perl libperl5.36 libsemanage2 libsepol2 libssl-dev libssl3 libstdc++-12-dev libtext-glob-perl libtiff6 libtsan2 libuv1 libwebp7 perl perl-modules-5.36 r-bioc-biocio r-bioc-keggrest r-cran-codetools r-cran-cpp11 r-cran-filelock r-cran-fs r-cran-mclust 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 hdf5-helpers hostname init-system-helpers libacl1 libaec-dev libaec0 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libblosc1 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 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhogweed6 libidn2-0 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev 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 libsnappy1v5 libss2 libssh2-1 libstdc++6 libsystemd0 libsz2 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-dnacopy r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-purecn r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib 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-bh r-cran-bit r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-formatr r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-hms r-cran-httr r-cran-isoband r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-processx r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo 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 283 upgraded, 41 newly installed, 1 to remove and 0 not upgraded. Need to get 281 MB of archives. After this operation, 179 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u5 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u4 [1897 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u4 [45.4 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u4 [2748 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u4 [606 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 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 6.1.76-1 [1930 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+b1 [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+b1 [166 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+b1 [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+b1 [111 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+b1 [1177 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+b2 [1491 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+b1 [94.4 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 252.22-1~deb12u1 [331 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.22-1~deb12u1 [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+deb12u2 [1404 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+b3 [46.6 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+b1 [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+b1 [28.8 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 3.0.11-1~deb12u2 [2019 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 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 [399 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 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:123 http://deb.debian.org/debian bookworm/main amd64 libasan6 amd64 11.3.0-12 [2050 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:126 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libblosc1 amd64 1.21.3+ds-1 [49.3 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:154 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u5 [390 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-10+deb12u5 [491 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.11-1~deb12u2 [2430 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:191 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libtsan0 amd64 11.3.0-12 [2016 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:208 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:212 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:220 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:229 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:232 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 r-bioc-bsgenome all 1.66.3-1 [6997 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:269 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 r-bioc-variantannotation amd64 1.44.1-1 [3642 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5lib amd64 1.20.0+dfsg-1 [102 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5filters amd64 1.10.0+dfsg-1 [120 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5 amd64 2.42.0+dfsg-1 [792 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 r-bioc-dnacopy amd64 1.72.3-1 [377 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 r-cran-data.table amd64 1.14.8+dfsg-1 [1683 kB] Get:289 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:291 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:295 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:296 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:297 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:298 http://deb.debian.org/debian bookworm/main amd64 r-cran-vgam amd64 1.1-7-1 [7230 kB] Get:299 http://deb.debian.org/debian bookworm/main amd64 r-cran-mclust amd64 6.0.0-1 [3945 kB] Get:300 http://deb.debian.org/debian bookworm/main amd64 r-bioc-purecn all 2.4.0+dfsg-1 [6025 kB] Get:301 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:302 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:303 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:304 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:305 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:306 http://deb.debian.org/debian bookworm/main amd64 r-cran-brio amd64 1.1.3-1+b1 [35.5 kB] Get:307 http://deb.debian.org/debian bookworm/main amd64 r-cran-ps amd64 1.7.2-1 [308 kB] Get:308 http://deb.debian.org/debian bookworm/main amd64 r-cran-processx amd64 3.8.0-1 [339 kB] Get:309 http://deb.debian.org/debian bookworm/main amd64 r-cran-callr all 3.7.3-2 [426 kB] Get:310 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:311 http://deb.debian.org/debian bookworm/main amd64 r-cran-rprojroot all 2.0.3-1 [119 kB] Get:312 http://deb.debian.org/debian bookworm/main amd64 r-cran-desc all 1.4.2-1 [348 kB] Get:313 http://deb.debian.org/debian bookworm/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB] Get:314 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:315 http://deb.debian.org/debian bookworm/main amd64 r-cran-evaluate all 0.20-1 [85.9 kB] Get:316 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:317 http://deb.debian.org/debian bookworm/main amd64 r-cran-fs amd64 1.6.1+dfsg-1 [226 kB] Get:318 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:319 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgbuild all 1.4.0-1 [187 kB] Get:320 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgload all 1.3.2-1 [206 kB] Get:321 http://deb.debian.org/debian bookworm/main amd64 r-cran-rstudioapi all 0.14-1 [281 kB] Get:322 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:323 http://deb.debian.org/debian bookworm/main amd64 r-cran-waldo all 0.4.0-1 [116 kB] Get:324 http://deb.debian.org/debian bookworm/main amd64 r-cran-testthat amd64 3.1.6-1 [1545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 281 MB in 5s (55.0 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 ... 38723 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u5_amd64.deb ... Unpacking base-files (12.4+deb12u5) over (11.1+deb11u9) ... Setting up base-files (12.4+deb12u5) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38723 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) over (1:4.4.18-4) ... Preparing to unpack .../libc6-dev_2.36-9+deb12u4_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Replacing files in old package libc6:amd64 (2.31-13+deb11u8) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u4_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../rpcsvc-proto_1.4.3-1_amd64.deb ... Unpacking rpcsvc-proto (1.4.3-1) ... Preparing to unpack .../libaudit-common_1%3a3.0.9-1_all.deb ... Unpacking libaudit-common (1:3.0.9-1) over (1:3.0-2) ... Setting up libaudit-common (1:3.0.9-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38733 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u4_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Setting up libc6:amd64 (2.36-9+deb12u4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38718 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u4_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u4) over (2.31-13+deb11u8) ... Setting up libc-bin (2.36-9+deb12u4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38718 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-1+b3_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.3-1+b3) over (0.7.9-2.2+b1) ... Setting up libcap-ng0:amd64 (0.8.3-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38720 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.9-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.0.9-1) over (1:3.0-2) ... Setting up libaudit1:amd64 (1:3.0.9-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38720 files and directories currently installed.) Preparing to unpack .../perl-base_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl-base (5.36.0-7+deb12u1) over (5.32.1-4+deb11u3) ... Setting up perl-base (5.36.0-7+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38723 files and directories currently installed.) Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.77) ... Setting up debconf (1.5.82) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38722 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-6+deb12u1_amd64.deb ... Unpacking libpam0g:amd64 (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam0g:amd64 (1.5.2-6+deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38722 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.33-2) over (1:4.4.18-4) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... (Reading database ... (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 ... 38722 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.1.76-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.76-1) over (5.10.209-2) ... Selecting previously unselected package gcc-12-base:amd64. Preparing to unpack .../gcc-12-base_12.2.0-14_amd64.deb ... Unpacking gcc-12-base:amd64 (12.2.0-14) ... Setting up gcc-12-base:amd64 (12.2.0-14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38767 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12.2.0-14_amd64.deb ... Unpacking libgcc-s1:amd64 (12.2.0-14) over (10.2.1-6) ... Setting up libgcc-s1:amd64 (12.2.0-14) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38767 files and directories currently installed.) Preparing to unpack .../libblkid1_2.38.1-5+b1_amd64.deb ... Unpacking libblkid1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libblkid1:amd64 (2.38.1-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38769 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-1) over (10.36-2+deb11u1) ... Setting up libpcre2-8-0:amd64 (10.42-1) ... (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 ... 38769 files and directories currently installed.) Preparing to unpack .../libselinux1_3.4-1+b6_amd64.deb ... Unpacking libselinux1:amd64 (3.4-1+b6) over (3.1-3) ... Setting up libselinux1:amd64 (3.4-1+b6) ... (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 ... 38770 files and directories currently installed.) Preparing to unpack .../libmount1_2.38.1-5+b1_amd64.deb ... Unpacking libmount1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libmount1:amd64 (2.38.1-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38772 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.38.1-5+b1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libsmartcols1:amd64 (2.38.1-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38774 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-1+b1_amd64.deb ... Unpacking login (1:4.13+dfsg1-1+b1) over (1:4.8.1-1) ... Setting up login (1:4.13+dfsg1-1+b1) ... 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 ... 38788 files and directories currently installed.) Preparing to unpack .../util-linux_2.38.1-5+b1_amd64.deb ... Unpacking util-linux (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... 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 Selecting previously unselected package util-linux-extra. Preparing to unpack .../util-linux-extra_2.38.1-5+b1_amd64.deb ... Unpacking util-linux-extra (2.38.1-5+b1) ... Setting up util-linux-extra (2.38.1-5+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38800 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.4.1-0.2) over (5.2.5-2.1~deb11u1) ... Setting up liblzma5:amd64 (5.4.1-0.2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38826 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 ... 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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 ... 38833 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 ... 38833 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 ... 38833 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u2_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u2) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38835 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 ... 38835 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 ... 38839 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 ... 38844 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 ... 38879 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 ... 38874 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 ... 38881 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 ... 38882 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 ... 38850 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 ... 38850 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.3+deb12u1_all.deb ... Unpacking debian-archive-keyring (2023.3+deb12u1) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.3+deb12u1) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38850 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1+b3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-1+b3) over (2.5.1-1+deb11u1) ... Setting up libseccomp2:amd64 (2.5.4-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38851 files and directories currently installed.) Preparing to unpack .../archives/apt_2.6.1_amd64.deb ... Unpacking apt (2.6.1) over (2.2.4) ... Setting up apt (2.6.1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38848 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.270_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.270) over (0.260) ... Setting up libdebconfclient0:amd64 (0.270) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38848 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.1_amd64.deb ... Unpacking base-passwd (3.6.1) over (3.5.51) ... Setting up base-passwd (3.6.1) ... Selecting previously unselected package perl-modules-5.36. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38848 files and directories currently installed.) Preparing to unpack .../perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg2-1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-1) over (5.3.28+dfsg1-0.8) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libperl5.36: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 ... 40270 files and directories currently installed.) Preparing to unpack .../libperl5.36_5.36.0-7+deb12u1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7+deb12u1) ... Selecting previously unselected package perl. Preparing to unpack .../perl_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl (5.36.0-7+deb12u1) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... (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 ... 40859 files and directories currently installed.) Preparing to unpack .../libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Setting up libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 40866 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 40881 files and directories currently installed.) Preparing to unpack .../usrmerge_37~deb12u1_all.deb ... Unpacking usrmerge (37~deb12u1) ... Setting up usrmerge (37~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 ... 40888 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.65.2_all.deb ... Unpacking init-system-helpers (1.65.2) over (1.60) ... Setting up init-system-helpers (1.65.2) ... (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 ... 40888 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4-4_all.deb ... Unpacking ncurses-base (6.4-4) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 40890 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2_amd64.deb ... Unpacking logsave (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.47.0-2_amd64.deb ... Unpacking libext2fs2:amd64 (1.47.0-2) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.47.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 40890 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2_amd64.deb ... Unpacking e2fsprogs (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../mount_2.38.1-5+b1_amd64.deb ... Unpacking mount (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Preparing to unpack .../libpam-runtime_1.5.2-6+deb12u1_all.deb ... Unpacking libpam-runtime (1.5.2-6+deb12u1) over (1.4.0-9+deb11u1) ... Setting up libpam-runtime (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 ... 40891 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-3_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-3) over (2.2.53-10) ... Setting up libacl1:amd64 (2.3.1-3) ... (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 ... 40892 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.1-4_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-4) over (1:2.4.48-6) ... Setting up libattr1:amd64 (1:2.5.1-4) ... Installing new version of config file /etc/xattr.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 ... 40893 files and directories currently installed.) Preparing to unpack .../libmd0_1.0.4-2_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-2) over (1.0.3-3) ... Setting up libmd0:amd64 (1.0.4-2) ... (Reading database ... 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Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-rhdf5 (2.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-cran-testthat (3.1.6-1) ... 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-purecn (2.4.0+dfsg-1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... 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. 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m57.4s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 1m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 1m57.7s DUMP: Package: r-bioc-purecn Version: 2.4.0+dfsg-1 Installed-Size: 6925 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biobase, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-cran-mclust, r-bioc-rhdf5, r-cran-matrix Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-r.utils, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-markdown, r-cran-rmarkdown, r-cran-testthat Description-en: copy number calling and SNV classification using targeted short read sequencing This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples. Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Homepage: https://bioconductor.org/packages/PureCN/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_2.4.0+dfsg-1_all.deb Size: 6025432 MD5sum: 63310446847d2c1ec0b260bf4a1f8c41 SHA256: 6fca9f573ba611b541592defbfa086a288b8b048dbddd6652560a56050a14dca 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 1m57.7s INFO: apt-cache knows about the following packages: r-bioc-purecn 1m57.7s INFO: Running scripts pre_install 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m57.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 1m57.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 1m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 1m57.8s DUMP: r-bioc-purecn: Installed: 2.4.0+dfsg-1 Candidate: 2.4.0+dfsg-1 Version table: *** 2.4.0+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m57.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 1m57.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 1m58.3s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-purecn is already the newest version (2.4.0+dfsg-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. 1m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 1m58.3s INFO: Running scripts post_install 1m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 1m58.4s INFO: Running scripts post_distupgrade 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_exceptions'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_exceptions'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_zz_backports'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_zz_backports'] 1m58.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 1m59.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 1m59.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpwrw8viat to sid 1m59.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m59.8s INFO: Running scripts pre_distupgrade 1m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_exceptions'] 1m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_exceptions'] 1m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m59.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m59.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m59.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m59.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 2m4.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9956 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7223 kB] Fetched 17.4 MB in 3s (5339 kB/s) Reading package lists... 2m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'update'] 2m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 3m4.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gcc-11-base gcc-12-base gcc-13-base hdf5-helpers libaec-dev libaec0 libasan6 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4-openssl-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-13-dev libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-cpp-103-1 libhwasan0 libice6 libicu67 libicu72 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery liblapack3 libldap-2.4-2 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.36 libpixman-1-0 libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsnappy1v5 libssh2-1t64 libssl-dev libstdc++-10-dev libstdc++-12-dev libstdc++-13-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff5 libtiff6 libtirpc-dev libtk8.6 libtsan0 libtsan2 libubsan1 libuv1 libwebp6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv perl-modules-5.36 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-dnacopy 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-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-hms r-cran-httr r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mclust r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-png r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-rematch2 r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto ucf unzip x11-common xdg-utils zip zlib1g-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost1.74-dev libcom-err2 libcurl4 libdb5.3 libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libhdf5-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libpng16-16 libpsl5 libreadline8 libss2 libssh2-1 libssl3 libtirpc3 libxt6 r-bioc-purecn r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib The following NEW packages will be installed: fonts-dejavu-mono gcc-13-base gcc-14-base libapt-pkg6.0t64 libboost1.83-dev libcom-err2t64 libcurl4t64 libdb5.3t64 libext2fs2t64 libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhdf5-103-1t64 libhwasan0 libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libss2t64 libssh2-1t64 libssl3t64 libstdc++-13-dev libtirpc3t64 libunistring5 libxt6t64 perl-modules-5.38 r-bioc-s4arrays r-bioc-sparsearray r-cran-abind r-cran-tidyr 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-10-base gcc-11-base gcc-12-base gcc-9-base gpgv grep hdf5-helpers hostname init-system-helpers libacl1 libaec-dev libaec0 libasan6 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libblosc1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcrypt-dev libcrypt1 libcurl4-openssl-dev libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-cpp-103-1 libhogweed6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libnettle8 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 libpcre2-8-0 libpcre3 libpixman-1-0 libquadmath0 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsnappy1v5 libssl-dev libstdc++-10-dev libstdc++-12-dev libstdc++6 libsystemd0 libsz2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan0 libtsan2 libubsan1 libudev1 libuuid1 libuv1 libwebp7 libx11-6 libx11-data libxft2 libxml2 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-dnacopy 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-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-blob r-cran-brio r-cran-cachem r-cran-cli r-cran-cpp11 r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-filelock r-cran-fs r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-hms r-cran-httr r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mclust r-cran-mgcv r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo 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 zlib1g zlib1g-dev 263 upgraded, 33 newly installed, 28 to remove and 0 not upgraded. Need to get 280 MB of archives. After this operation, 112 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-10 [97.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3 [66.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [189 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcurl4-openssl-dev amd64 8.6.0-3.2 [534 kB] Get:13 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1 [786 kB] Get:14 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.0+dfsg-1 [176 kB] Get:15 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.62.0-1 [2119 kB] Get:16 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2062 kB] Get:17 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.36.0-1 [2258 kB] Get:18 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.2-1 [824 kB] Get:19 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240303-1 [42.8 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240303-1 [72.2 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240303-1 [713 kB] Get:22 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:23 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:24 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:25 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:26 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:27 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:28 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get:29 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.4-1 [1159 kB] Get:30 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:31 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get:32 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libssl-dev amd64 3.1.5-1.1 [2474 kB] Get:34 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.6.0-3.2 [430 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:37 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.1.1+dfsg-2 [397 kB] Get:38 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:39 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:40 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:41 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get:42 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.42.0-1 [622 kB] Get:43 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB] Get:44 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3848 kB] Get:45 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.7 MB] Get:46 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB] Get:47 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.64.1-1 [4705 kB] Get:48 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240303-1 [836 kB] Get:51 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:52 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get:53 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:54 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [504 kB] Get:55 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.2.0-1 [484 kB] Get:56 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get:57 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1196 kB] Get:58 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1794 kB] Get:59 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1827 kB] Get:60 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1139 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:62 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:64 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.16.1-1 [1751 kB] Get:65 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-18 [43.5 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240303-1 [136 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240303-1 [25.9 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240303-1 [9208 B] Get:69 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240303-1 [2723 kB] Get:70 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240303-1 [1201 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240303-1 [1071 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.3.0-15 [2069 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240303-1 [147 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.3.0-15 [2435 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240303-1 [2455 kB] Get:76 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-15 [41.8 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240303-1 [1485 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-18 [2544 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-18 [2211 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:81 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2.1 [10.6 MB] Get:82 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:83 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.36.0-1 [1337 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:85 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3 [1285 kB] Get:86 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1 [3580 kB] Get:87 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2144 kB] Get:88 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.12.0+dfsg-1 [214 kB] Get:89 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5094 kB] Get:90 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:91 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:92 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:93 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.3-1 [861 kB] Get:94 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:95 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.34-1 [192 kB] Get:96 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:97 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:98 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:99 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:100 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:101 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:102 http://deb.debian.org/debian sid/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:103 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:104 http://deb.debian.org/debian sid/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get:105 http://deb.debian.org/debian sid/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:106 http://deb.debian.org/debian sid/main amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [301 kB] Get:107 http://deb.debian.org/debian sid/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get:108 http://deb.debian.org/debian sid/main amd64 r-bioc-biomart all 2.58.2+dfsg-1 [450 kB] Get:109 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.54.3+dfsg-1 [1665 kB] Get:110 http://deb.debian.org/debian sid/main amd64 r-bioc-dnacopy amd64 1.76.0-1 [380 kB] Get:111 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.70.2-1 [6977 kB] Get:112 http://deb.debian.org/debian sid/main amd64 r-bioc-variantannotation amd64 1.48.1-1 [3500 kB] Get:113 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1 [215 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5.1 [135 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5.1 [333 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5.1 [79.6 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5.1 [33.0 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libcom-err2t64 amd64 1.47.0-2.3+b1 [20.5 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.3+b1 [206 kB] Get:125 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.3+b1 [20.2 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libss2t64 amd64 1.47.0-2.3+b1 [25.2 kB] Get:127 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.3+b1 [572 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:129 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2+b1 [296 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13+b1 [984 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:135 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1 [364 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1 [125 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b1 [10.2 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:143 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:148 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.1 [2904 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [697 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1 [72.7 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [48.5 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.1 [4278 kB] Get:153 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.1 [236 kB] Get:154 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.1 [1644 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:158 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:161 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:163 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:164 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:165 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:166 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1 [1425 kB] Get:172 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13+b1 [1368 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2+b1 [328 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:176 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:177 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:178 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1 [317 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1 [388 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-3 [278 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.0+ds-1 [48.0 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.0+ds-1 [216 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.0+ds-1 [35.0 kB] Get:192 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1 [462 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-3 [1453 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-10 [159 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-10 [191 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-3.1 [167 kB] Get:201 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3.1 [69.2 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-cran-ps amd64 1.7.6-1 [310 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2+b2 [290 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:207 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [108 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4 [308 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:213 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:217 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-2 [26.8 MB] Get:219 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:220 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:221 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.7.7-1 [2251 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:224 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:225 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:226 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.5 [1510 kB] Get:227 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:228 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:229 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:230 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:231 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:232 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:233 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:234 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-10 [117 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-10 [30.1 kB] Get:237 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-10 [155 kB] Get:238 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-10 [1231 kB] Get:239 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:240 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:241 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:242 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:243 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-10 [143 kB] Get:244 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:248 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:249 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libtsan0 amd64 11.4.0-7 [2019 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libasan6 amd64 11.4.0-7 [2049 kB] Get:252 http://deb.debian.org/debian sid/main amd64 gcc-11-base amd64 11.4.0-7 [40.3 kB] Get:253 http://deb.debian.org/debian sid/main amd64 libstdc++-10-dev amd64 10.5.0-3 [1755 kB] Get:254 http://deb.debian.org/debian sid/main amd64 libgcc-10-dev amd64 10.5.0-3 [2323 kB] Get:255 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-3 [36.6 kB] Get:256 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:257 http://deb.debian.org/debian sid/main amd64 hdf5-helpers amd64 1.10.10+repack-3.1 [23.3 kB] Get:258 http://deb.debian.org/debian sid/main amd64 libaec-dev amd64 1.1.2-1 [20.9 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.2-1 [23.4 kB] Get:260 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.2-1 [7684 B] Get:261 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libblosc1 amd64 1.21.5+ds-1+b1 [49.6 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.1-1 [129 kB] Get:264 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1 [1242 kB] Get:265 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-103-1 amd64 1.10.10+repack-3+b1 [131 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libjpeg-dev amd64 1:2.1.5-2+b2 [72.1 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:268 http://deb.debian.org/debian sid/main amd64 libuv1 amd64 1.48.0-1 [147 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.19-1 [99.8 kB] Get:270 http://deb.debian.org/debian sid/main amd64 littler all 0.3.19-1 [15.4 kB] Get:271 http://deb.debian.org/debian sid/main amd64 r-cran-brio amd64 1.1.4-1 [37.4 kB] Get:272 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.0.8-1 [72.0 kB] Get:273 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.14.10+dfsg-1 [1716 kB] Get:274 http://deb.debian.org/debian sid/main amd64 r-cran-desc all 1.4.3-1 [351 kB] Get:275 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 0.23-1 [90.6 kB] Get:276 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.3+dfsg-1 [227 kB] Get:277 http://deb.debian.org/debian sid/main amd64 r-cran-gtable all 0.3.4+dfsg-1 [221 kB] Get:278 http://deb.debian.org/debian sid/main amd64 r-cran-mass amd64 7.3-60.0.1-1 [1118 kB] Get:279 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.164-1 [2280 kB] Get:280 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:282 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:283 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:284 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3405 kB] Get:285 http://deb.debian.org/debian sid/main amd64 r-cran-mclust amd64 6.0.1-1 [3945 kB] Get:286 http://deb.debian.org/debian sid/main amd64 r-cran-processx amd64 3.8.3-1 [345 kB] Get:287 http://deb.debian.org/debian sid/main amd64 r-cran-pkgbuild all 1.4.3-1 [210 kB] Get:288 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:289 http://deb.debian.org/debian sid/main amd64 r-cran-rprojroot all 2.0.4-1 [124 kB] Get:290 http://deb.debian.org/debian sid/main amd64 r-cran-pkgload all 1.3.4-1 [208 kB] Get:291 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] Get:292 http://deb.debian.org/debian sid/main amd64 r-cran-rstudioapi all 0.15.0-1 [282 kB] Get:293 http://deb.debian.org/debian sid/main amd64 r-cran-waldo all 0.5.2-1 [120 kB] Get:294 http://deb.debian.org/debian sid/main amd64 r-cran-testthat amd64 3.2.1-1 [1644 kB] Get:295 http://deb.debian.org/debian sid/main amd64 r-cran-vgam amd64 1.1-9-1 [7329 kB] Get:296 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.8-1 [106 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 280 MB in 5s (61.4 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 ... 42866 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (12.4+deb12u5) ... Setting up base-files (13) ... 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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Unpacking r-cran-curl (5.2.0+dfsg-1) over (5.0.0+dfsg-1) ... Preparing to unpack .../3-r-bioc-biobase_2.62.0-1_amd64.deb ... Unpacking r-bioc-biobase (2.62.0-1) over (2.58.0-2) ... Preparing to unpack .../4-r-bioc-s4vectors_0.40.2+dfsg-1_amd64.deb ... Unpacking r-bioc-s4vectors (0.40.2+dfsg-1) over (0.36.1-1) ... Preparing to unpack .../5-r-bioc-iranges_2.36.0-1_amd64.deb ... Unpacking r-bioc-iranges (2.36.0-1) over (2.32.0-1) ... Preparing to unpack .../6-r-cran-dbi_1.2.2-1_all.deb ... Unpacking r-cran-dbi (1.2.2-1) over (1.1.3-1) ... Selecting previously unselected package gcc-14-base:amd64. Preparing to unpack .../7-gcc-14-base_14-20240303-1_amd64.deb ... Unpacking gcc-14-base:amd64 (14-20240303-1) ... Setting up gcc-14-base:amd64 (14-20240303-1) ... (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 ... 42884 files and directories currently installed.) Preparing to unpack .../libstdc++6_14-20240303-1_amd64.deb ... Unpacking libstdc++6:amd64 (14-20240303-1) over (12.2.0-14) ... Setting up libstdc++6:amd64 (14-20240303-1) ... (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 ... 42884 files and directories currently installed.) Preparing to unpack .../00-r-cran-rlang_1.1.3-1_amd64.deb ... Unpacking r-cran-rlang (1.1.3-1) over (1.0.6-1) ... Preparing to unpack .../01-r-cran-cli_3.6.2-1_amd64.deb ... Unpacking r-cran-cli (3.6.2-1) over (3.6.0-1) ... Preparing to unpack .../02-r-cran-glue_1.7.0-1_amd64.deb ... Unpacking r-cran-glue (1.7.0-1) over (1.6.2-1) ... Preparing to unpack .../03-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45238 files and directories currently installed.) Preparing to unpack .../libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../libssh2-1t64_1.11.0-4.1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1) ... Preparing to unpack .../libzstd1_1.5.5+dfsg2-2_amd64.deb ... Unpacking libzstd1:amd64 (1.5.5+dfsg2-2) over (1.5.4+dfsg2-5) ... Setting up libzstd1:amd64 (1.5.5+dfsg2-2) ... (Reading database ... (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 ... 45254 files and directories currently installed.) Preparing to unpack .../libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b6) ... Preparing to unpack .../libgssapi-krb5-2_1.20.1-5.1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-5.1) over (1.20.1-2+deb12u1) ... Preparing to unpack .../libkrb5-3_1.20.1-5.1_amd64.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45263 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.3+b1_amd64.deb ... Unpacking e2fsprogs (1.47.0-2.3+b1) 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 Preparing to unpack .../libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.3-2) ... 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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 ... 45214 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.13+b1_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.13+b1) ... Setting up libapt-pkg6.0t64:amd64 (2.7.13+b1) ... (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 ... 45266 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-5) over (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45266 files and directories currently installed.) Preparing to unpack .../libsystemd0_255.4-1_amd64.deb ... Unpacking libsystemd0:amd64 (255.4-1) over (252.22-1~deb12u1) ... Setting up libsystemd0:amd64 (255.4-1) ... (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 ... 45266 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1_amd64.deb ... Unpacking libudev1:amd64 (255.4-1) over (252.22-1~deb12u1) ... Setting up libudev1:amd64 (255.4-1) ... (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 ... 45266 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2+b1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2+b1) over (0.8.1-1) ... Setting up libxxhash0:amd64 (0.8.2-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45267 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271+b1_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271+b1) over (0.270) ... Setting up libdebconfclient0:amd64 (0.271+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45268 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45269 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45269 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (Reading database ... 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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 ... 45269 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.4-2) ... (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 ... 45268 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-2.1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-2.1) ... (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 ... 45268 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-4) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45268 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-3.1_amd64.deb ... Unpacking perl (5.38.2-3.1) over (5.36.0-7+deb12u1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.1_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.1) ... 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 ... 46681 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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Unpacking perl-base (5.38.2-3.1) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47206 files and directories currently installed.) Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) over (2.1.28+dfsg-10) ... Preparing to unpack .../libpam-modules-bin_1.5.3-6_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47205 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-6) 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 (1.5.3-6) ... Installing new version of config file /etc/security/namespace.init ... (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 ... 47202 files and directories currently installed.) Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.82) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... 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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 ... 47194 files and directories currently installed.) Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-4+b1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) over (2.1.28+dfsg-10) ... Preparing to unpack .../libldap-2.5-0_2.5.13+dfsg-5+b3_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) over (2.5.13+dfsg-5) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: librtmp1:amd64 depends on libgnutls30 (>= 3.6.14). libldap-2.5-0:amd64 depends on libgnutls30 (>= 3.8.2). libldap-2.4-2:amd64 depends on libgnutls30 (>= 3.7.0). apt depends on libgnutls30 (>= 3.7.5). (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 ... 47195 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u2) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47166 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1) ... (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 ... 47194 files and directories currently installed.) Preparing to unpack .../0-libnghttp2-14_1.59.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1) over (1.52.0-1+deb12u1) ... Preparing to unpack .../1-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) over (2.37-6) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../2-fonts-dejavu-mono_2.37-8_all.deb ... 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Unpacking libblkid1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-10) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47214 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-10_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.3-10) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libreadline8 (>= 6.0). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47213 files and directories currently installed.) Removing libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libreadline8t64:amd64. (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 (8.2-3.1) ... Preparing to unpack .../readline-common_8.2-3.1_all.deb ... Unpacking readline-common (8.2-3.1) over (8.2-1.3) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4-4) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... dpkg: libxt6:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libxt6. (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 ... 47221 files and directories currently installed.) Removing libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package libxt6t64:amd64. (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 ... 46465 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 .../libc-bin_2.37-15.1_amd64.deb ... Unpacking libc-bin (2.37-15.1) over (2.36-9+deb12u4) ... Setting up libc-bin (2.37-15.1) ... Setting up libssl3t64:amd64 (3.1.5-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 48126 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3+b1_amd64.deb ... Unpacking coreutils (9.4-3+b1) over (9.1-1) ... Setting up coreutils (9.4-3+b1) ... (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 ... 48120 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-2_amd64.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (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 ... 48120 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-10_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-10) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-10) ... (Reading database ... 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Current default time zone: 'Etc/UTC' Local time is now: Tue Mar 5 11:47:31 UTC 2024. Universal Time is now: Tue Mar 5 11:47:31 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up gcc-10-base:amd64 (10.5.0-3) ... Setting up libpcre3:amd64 (2:8.39-15+b1) ... Setting up libglib2.0-0t64:amd64 (2.78.4-3) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... Setting up libuv1:amd64 (1.48.0-1) ... Setting up gcc-13-base:amd64 (13.2.0-18) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libquadmath0:amd64 (14-20240303-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.1.5-1.1) ... Setting up libpng16-16t64:amd64 (1.6.43-3) ... Setting up libatomic1:amd64 (14-20240303-1) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... 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Setting up libthai-data (0.1.29-2) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-5.1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1) ... Setting up libtsan2:amd64 (14-20240303-1) ... Setting up libc-dev-bin (2.37-15.1) ... Setting up openssl (3.1.5-1.1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up readline-common (8.2-3.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up liblsan0:amd64 (14-20240303-1) ... Setting up libsz2:amd64 (1.1.2-1) ... Setting up libitm1:amd64 (14-20240303-1) ... Setting up gcc-9-base:amd64 (9.5.0-5) ... Setting up libtsan0:amd64 (11.4.0-7) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up fontconfig-config (2.15.0-1) ... Setting up libgcc-10-dev:amd64 (10.5.0-3) ... Setting up libaec-dev:amd64 (1.1.2-1) ... Setting up e2fsprogs (1.47.0-2.3+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 8 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up libgcc-12-dev:amd64 (12.3.0-15) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5.1) ... Setting up libreadline8t64:amd64 (8.2-3.1) ... Setting up libgcc-13-dev:amd64 (13.2.0-18) ... Setting up libc6-dev:amd64 (2.37-15.1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libfontconfig1:amd64 (2.15.0-1) ... Setting up libstdc++-13-dev:amd64 (13.2.0-18) ... Setting up fontconfig (2.15.0-1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost1.83-dev:amd64 (1.83.0-2.1) ... Setting up libstdc++-10-dev:amd64 (10.5.0-3) ... Setting up libcurl4t64:amd64 (8.6.0-3.2) ... Setting up libstdc++-12-dev:amd64 (12.3.0-15) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libpango-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) ... Setting up libcurl4-openssl-dev:amd64 (8.6.0-3.2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2+b2) ... Setting up r-base-core (4.3.3-2) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-5-1) ... Setting up r-cran-ps (1.7.6-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up r-cran-xml (3.99-0.16.1-1) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.10+repack-3+b1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-rcurl (1.98-1.14+dfsg-1) ... Setting up r-cran-filelock (1.0.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.11-2) ... Setting up r-cran-littler (0.3.19-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.3+dfsg-1) ... Setting up r-cran-rcpp (1.0.12-1) ... Setting up r-cran-curl (5.2.0+dfsg-1) ... Setting up r-cran-brio (1.1.4-1) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up r-cran-rlang (1.1.3-1) ... Setting up r-cran-matrixstats (1.2.0-1) ... Setting up littler (0.3.19-1) ... Setting up r-bioc-matrixgenerics (1.14.0-1) ... Setting up r-cran-vgam (1.1-9-1) ... Setting up r-cran-sys (3.4.2-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up r-cran-processx (3.8.3-1) ... Setting up r-cran-abind (1.4-5-2) ... Setting up r-cran-digest (0.6.34-1) ... Setting up r-cran-yaml (2.3.8-1) ... Setting up r-cran-evaluate (0.23-1) ... Setting up r-cran-dbi (1.2.2-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-mclust (6.0.1-1) ... Setting up r-cran-data.table (1.14.10+dfsg-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-rprojroot (2.0.4-1) ... Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ... Setting up r-cran-askpass (1.2.0-1) ... Setting up r-bioc-biobase (2.62.0-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-rstudioapi (0.15.0-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.3-1) ... Setting up r-cran-cpp11 (0.4.7-1) ... Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-gtable (0.3.4+dfsg-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up r-cran-cachem (1.0.8-1) ... Setting up r-bioc-iranges (2.36.0-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-openssl (2.1.1+dfsg-2) ... Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biocparallel (1.36.0-1) ... Setting up r-bioc-rhtslib (2.4.1+dfsg-3) ... Setting up r-cran-desc (1.4.3-1) ... Setting up r-cran-xml2 (1.3.6-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-bioc-biocio (1.12.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-waldo (0.5.2-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.42.0-1) ... Setting up r-cran-pkgbuild (1.4.3-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up r-cran-rsqlite (2.3.4-1) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-pkgload (1.3.4-1) ... Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ... Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ... Setting up r-bioc-biostrings (2.70.2+dfsg-1) ... Setting up r-cran-testthat (3.2.1-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-bioc-rsamtools (2.18.0+dfsg-1) ... Setting up r-cran-dbplyr (2.4.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... Setting up r-bioc-biocfilecache (2.10.1+dfsg-1) ... Setting up r-bioc-keggrest (1.42.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.64.1-1) ... Setting up r-bioc-biomart (2.58.2+dfsg-1) ... Setting up r-bioc-genomicalignments (1.38.2-1) ... Setting up r-bioc-rtracklayer (1.62.0-1) ... Setting up r-bioc-genomicfeatures (1.54.3+dfsg-1) ... Setting up r-bioc-bsgenome (1.70.2-1) ... Setting up r-bioc-variantannotation (1.48.1-1) ... Processing triggers for debianutils (5.17) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 3m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-yf', 'dist-upgrade'] 3m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m6.2s DUMP: 544743b355177689dee4bc800f012fe9 - 3m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 3m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 3m6.5s DUMP: Package: r-bioc-purecn Version: 2.8.1+dfsg-1 Installed-Size: 6916 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-dnacopy, r-bioc-variantannotation (>= 1.14.1), r-bioc-genomicranges (>= 1.20.3), r-bioc-iranges (>= 2.2.1), r-cran-rcolorbrewer, r-bioc-s4vectors, r-cran-data.table, r-bioc-summarizedexperiment, r-bioc-genomeinfodb, r-bioc-genomicfeatures, r-bioc-rsamtools, r-bioc-biobase, r-bioc-biostrings, r-bioc-biocgenerics, r-bioc-rtracklayer, r-cran-ggplot2, r-cran-gridextra, r-cran-futile.logger, r-cran-vgam, r-cran-mclust, r-bioc-rhdf5, r-cran-matrix Suggests: r-bioc-biocparallel, r-bioc-biocstyle, r-cran-pscbs, r-cran-r.utils, r-cran-covr, r-cran-knitr, r-cran-optparse, r-bioc-org.hs.eg.db, r-cran-jsonlite, r-cran-markdown, r-cran-rmarkdown, r-cran-testthat Description-en: copy number calling and SNV classification using targeted short read sequencing This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples. Description-md5: 8e04360f54e8e8be0dd9281fc8ab5c7b Homepage: https://bioconductor.org/packages/PureCN/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-purecn/r-bioc-purecn_2.8.1+dfsg-1_all.deb Size: 6014792 MD5sum: 6b7c7e0737b43e56d12dff8140d3cb1e SHA256: a9b3c22616d7d02647cea2819e03e91b8b661c0630be685f414889594a60ec24 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 3m6.5s INFO: apt-cache knows about the following packages: r-bioc-purecn 3m6.5s INFO: Running scripts pre_install 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 3m6.6s 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: 3m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 3m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 3m6.6s DUMP: r-bioc-purecn: Installed: (none) Candidate: 2.8.1+dfsg-1 Version table: 2.8.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 3m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 3m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 3m10.1s DUMP: Reading package lists... Building dependency tree... Reading state information... 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-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib Suggested packages: libhdf5-doc r-bioc-biocstyle r-cran-pscbs r-cran-r.utils r-cran-covr r-cran-knitr r-cran-optparse r-bioc-org.hs.eg.db r-cran-markdown r-cran-rmarkdown r-cran-bench r-cran-mockery r-cran-tinytest The following packages will be REMOVED: libhdf5-cpp-103-1 The following NEW packages will be installed: libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 r-bioc-purecn r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib 0 upgraded, 10 newly installed, 1 to remove and 0 not upgraded. Need to get 10.1 MB of archives. After this operation, 23.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.1 [131 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.1 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.1 [63.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.1 [40.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.1 [21.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libhdf5-dev amd64 1.10.10+repack-3.1 [2640 kB] Get:7 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5lib amd64 1.24.2+dfsg-1 [103 kB] Get:8 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5filters amd64 1.14.1+dfsg-3 [139 kB] Get:9 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5 amd64 2.46.1+dfsg-1 [848 kB] Get:10 http://deb.debian.org/debian sid/main amd64 r-bioc-purecn all 2.8.1+dfsg-1 [6015 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.1 MB in 1s (7305 kB/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 ... 48180 files and directories currently installed.) Removing libhdf5-cpp-103-1:amd64 (1.10.10+repack-3+b1) ... Selecting previously unselected package libhdf5-cpp-103-1t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 48171 files and directories currently installed.) Preparing to unpack .../0-libhdf5-cpp-103-1t64_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1) ... Selecting previously unselected package libhdf5-fortran-102t64:amd64. Preparing to unpack .../1-libhdf5-fortran-102t64_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.1) ... Selecting previously unselected package libhdf5-hl-100t64:amd64. Preparing to unpack .../2-libhdf5-hl-100t64_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1) ... Selecting previously unselected package libhdf5-hl-fortran-100t64:amd64. Preparing to unpack .../3-libhdf5-hl-fortran-100t64_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.1) ... Selecting previously unselected package libhdf5-hl-cpp-100t64:amd64. Preparing to unpack .../4-libhdf5-hl-cpp-100t64_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../5-libhdf5-dev_1.10.10+repack-3.1_amd64.deb ... Unpacking libhdf5-dev (1.10.10+repack-3.1) ... Selecting previously unselected package r-bioc-rhdf5lib. Preparing to unpack .../6-r-bioc-rhdf5lib_1.24.2+dfsg-1_amd64.deb ... Unpacking r-bioc-rhdf5lib (1.24.2+dfsg-1) ... Selecting previously unselected package r-bioc-rhdf5filters. Preparing to unpack .../7-r-bioc-rhdf5filters_1.14.1+dfsg-3_amd64.deb ... Unpacking r-bioc-rhdf5filters (1.14.1+dfsg-3) ... Selecting previously unselected package r-bioc-rhdf5. Preparing to unpack .../8-r-bioc-rhdf5_2.46.1+dfsg-1_amd64.deb ... Unpacking r-bioc-rhdf5 (2.46.1+dfsg-1) ... Selecting previously unselected package r-bioc-purecn. Preparing to unpack .../9-r-bioc-purecn_2.8.1+dfsg-1_all.deb ... Unpacking r-bioc-purecn (2.8.1+dfsg-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.1) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.1) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.1) ... Setting up libhdf5-dev (1.10.10+repack-3.1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up r-bioc-rhdf5lib (1.24.2+dfsg-1) ... Setting up r-bioc-rhdf5filters (1.14.1+dfsg-3) ... Setting up r-bioc-rhdf5 (2.46.1+dfsg-1) ... Setting up r-bioc-purecn (2.8.1+dfsg-1) ... Processing triggers for libc-bin (2.37-15.1) ... 3m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 3m10.1s INFO: Running scripts post_install 3m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 3m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 3m10.1s INFO: Running scripts post_distupgrade 3m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_base_cleanup'] 3m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_exceptions'] 3m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_exceptions'] 3m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 3m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_squeeze-backports'] 3m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_zz_backports'] 3m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_distupgrade_zz_backports'] 3m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m11.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m11.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m12.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m12.9s INFO: Running scripts pre_install 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_database-server'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_exceptions'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_extras'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_install_foreign_architecture_i386'] 3m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 3m13.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 3m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy'] 3m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 3m13.0s DUMP: r-bioc-purecn: Installed: 2.8.1+dfsg-1 Candidate: 2.8.1+dfsg-1 Version table: *** 2.8.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 3m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-cache', 'policy', 'r-bioc-purecn'] 3m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn=2.8.1+dfsg-1'] 3m13.7s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-purecn is already the newest version (2.8.1+dfsg-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-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 3m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', 'install', 'r-bioc-purecn=2.8.1+dfsg-1'] 3m13.7s INFO: Running scripts post_install 3m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 3m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_install_exceptions'] 3m13.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m15.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m15.3s INFO: /bin converted to /usr/bin by /usr merge 3m15.3s INFO: /lib converted to /usr/lib by /usr merge 3m15.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 3m15.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 3m15.3s INFO: /sbin converted to /usr/sbin by /usr merge 3m17.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', '-ac', '--ignore-obsolete'] 3m22.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', '-ac', '--ignore-obsolete'] 3m22.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 3m22.4s DUMP: 0.15.6 3m22.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 3m22.4s INFO: Running adequate version 0.15.6 now. 3m22.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'r-bioc-purecn'] 3m22.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'r-bioc-purecn'] 3m22.6s INFO: Running scripts pre_remove 3m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 3m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 3m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 3m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 3m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m32.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 3m32.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 3m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 3m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_exceptions'] 3m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/pre_remove_exceptions'] 3m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m33.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.13+b1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-10 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.5 install ok installed e2fsprogs e2fsprogs 1.47.0-2.3+b1 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1 install ok installed fontconfig-config fontconfig-config 2.15.0-1 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 gcc-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-11-base:amd64 gcc-11-base 11.4.0-7 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-15 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-18 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240303-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hdf5-helpers hdf5-helpers 1.10.10+repack-3.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaec-dev:amd64 libaec-dev 1.1.2-1 install ok installed libaec0:amd64 libaec0 1.1.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libasan6:amd64 libasan6 11.4.0-7 install ok installed libasan8:amd64 libasan8 14-20240303-1 install ok installed libatomic1:amd64 libatomic1 14-20240303-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-10 install ok installed libblosc1:amd64 libblosc1 1.21.5+ds-1+b1 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-2.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc-dev-bin libc-dev-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libc6-dev:amd64 libc6-dev 2.37-15.1 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.3+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl4-openssl-dev:amd64 libcurl4-openssl-dev 8.6.0-3.2 install ok installed libcurl4t64:amd64 libcurl4t64 8.6.0-3.2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.3+b1 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 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-10-dev:amd64 libgcc-10-dev 10.5.0-3 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.3.0-15 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-18 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240303-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1 install ok installed libgfortran5:amd64 libgfortran5 14-20240303-1 deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 2.74.6-2 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgomp1:amd64 libgomp1 14-20240303-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5.1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-3.1 install ok installed libhdf5-cpp-103-1t64:amd64 libhdf5-cpp-103-1t64 1.10.10+repack-3.1 install ok installed libhdf5-dev libhdf5-dev 1.10.10+repack-3.1 install ok installed libhdf5-fortran-102t64:amd64 libhdf5-fortran-102t64 1.10.10+repack-3.1 install ok installed libhdf5-hl-100t64:amd64 libhdf5-hl-100t64 1.10.10+repack-3.1 install ok installed libhdf5-hl-cpp-100t64:amd64 libhdf5-hl-cpp-100t64 1.10.10+repack-3.1 install ok installed libhdf5-hl-fortran-100t64:amd64 libhdf5-hl-fortran-100t64 1.10.10+repack-3.1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libhwasan0:amd64 libhwasan0 14-20240303-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libitm1:amd64 libitm1 14-20240303-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg-dev:amd64 libjpeg-dev 1:2.1.5-2+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjpeg62-turbo-dev:amd64 libjpeg62-turbo-dev 1:2.1.5-2+b2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5.1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5.1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5.1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 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 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblsan0:amd64 liblsan0 14-20240303-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-10 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.0+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.0+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.0+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 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 5.38.2-3.1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-3 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libquadmath0:amd64 libquadmath0 14-20240303-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-3.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-10 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.10-1+b1 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.3+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1 install ok installed libssl-dev:amd64 libssl-dev 3.1.5-1.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++-10-dev:amd64 libstdc++-10-dev 10.5.0-3 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.3.0-15 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-18 install ok installed libstdc++6:amd64 libstdc++6 14-20240303-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1 install ok installed libsz2:amd64 libsz2 1.1.2-1 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 libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.1 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.1 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtsan0:amd64 libtsan0 11.4.0-7 install ok installed libtsan2:amd64 libtsan2 14-20240303-1 install ok installed libubsan1:amd64 libubsan1 14-20240303-1 install ok installed libudev1:amd64 libudev1 255.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-10 install ok installed libuv1:amd64 libuv1 1.48.0-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.7.7-1 install ok installed littler littler 0.3.19-1 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.3+b1 install ok installed lsb-base lsb-base 11.6 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-10 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.1 install ok installed perl-base perl-base 5.38.2-3.1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.1 install ok installed r-base-core r-base-core 4.3.3-2 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.64.1-1 install ok installed r-bioc-biobase r-bioc-biobase 2.62.0-1 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.10.1+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.48.1-2 install ok installed r-bioc-biocio r-bioc-biocio 1.12.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.36.0-1 install ok installed r-bioc-biomart r-bioc-biomart 2.58.2+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.70.2+dfsg-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.70.2-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.28.0+dfsg-1 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.76.0-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.38.6+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.11-2 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.38.2-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.54.3+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.54.1+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.36.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.42.0+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.14.0-1 install ok installed r-bioc-purecn r-bioc-purecn 2.8.1+dfsg-1 install ok installed r-bioc-rhdf5 r-bioc-rhdf5 2.46.1+dfsg-1 install ok installed r-bioc-rhdf5filters r-bioc-rhdf5filters 1.14.1+dfsg-3 install ok installed r-bioc-rhdf5lib r-bioc-rhdf5lib 1.24.2+dfsg-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.4.1+dfsg-3 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.18.0+dfsg-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.62.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.2.0+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.40.2+dfsg-1 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.2.4+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.32.0+dfsg-1 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.48.1-1 install ok installed r-bioc-xvector r-bioc-xvector 0.42.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.48.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 install ok installed r-cran-askpass r-cran-askpass 1.2.0-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-brio r-cran-brio 1.1.4-1 install ok installed r-cran-cachem r-cran-cachem 1.0.8-1 install ok installed r-cran-callr r-cran-callr 3.7.3-2 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-codetools r-cran-codetools 0.2-19-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-0+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.4.7-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.2.0+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.14.10+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.2.2-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.4.0+dfsg-1 install ok installed r-cran-desc r-cran-desc 1.4.3-1 install ok installed r-cran-diffobj r-cran-diffobj 0.3.5-1+b1 install ok installed r-cran-digest r-cran-digest 0.6.34-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-evaluate r-cran-evaluate 0.23-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-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-formatr r-cran-formatr 1.14-1 install ok installed r-cran-fs r-cran-fs 1.6.3+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-ggplot2 r-cran-ggplot2 3.4.4+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.4+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.22-5-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.19-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.2.0-1 install ok installed r-cran-mclust r-cran-mclust 6.0.1-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.164-1 install ok installed r-cran-openssl r-cran-openssl 2.1.1+dfsg-2 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.4.3-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-pkgload r-cran-pkgload 1.3.4-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-png r-cran-png 0.1-8-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-processx r-cran-processx 3.8.3-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-ps r-cran-ps 1.7.6-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.12-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.14+dfsg-1 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.4-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.4-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.15.0-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-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-testthat r-cran-testthat 3.2.1-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-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-vgam r-cran-vgam 1.1-9-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-waldo r-cran-waldo 0.5.2-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.16.1-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.6-1 install ok installed r-cran-yaml r-cran-yaml 2.3.8-1 install ok installed readline-common readline-common 8.2-3.1 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 0.0.22 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-10 install ok installed util-linux-extra util-linux-extra 2.39.3-10 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3.1 3m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 3m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libtirpc3:amd64=1.3.4+ds-1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'gcc-11-base:amd64-', 'gcc-13-base:amd64-', 'hdf5-helpers-', 'libaec-dev:amd64-', 'libaec0:amd64-', 'libasan6:amd64-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libblas3:amd64-', 'libblosc1:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4-openssl-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-13-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-cpp-103-1t64:amd64-', 'libhdf5-dev-', 'libhdf5-fortran-102t64:amd64-', 'libhdf5-hl-100t64:amd64-', 'libhdf5-hl-cpp-100t64:amd64-', 'libhdf5-hl-fortran-100t64:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libitm1:amd64-', 'libjbig0:amd64-', 'libjpeg-dev:amd64-', 'libjpeg62-turbo:amd64-', 'libjpeg62-turbo-dev:amd64-', 'libjs-jquery-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblsan0: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-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsnappy1v5:amd64-', 'libssh2-1t64:amd64-', 'libssl-dev:amd64-', 'libstdc++-10-dev:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libtsan0:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libuv1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'littler-', 'node-html5shiv-', 'openssl-', '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-dnacopy-', '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-rhdf5-', 'r-bioc-rhdf5filters-', 'r-bioc-rhdf5lib-', 'r-bioc-rhtslib-', 'r-bioc-rsamtools-', 'r-bioc-rtracklayer-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-summarizedexperiment-', 'r-bioc-variantannotation-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-askpass-', 'r-cran-assertthat-', 'r-cran-bh-', 'r-cran-bit-', 'r-cran-bit64-', 'r-cran-bitops-', 'r-cran-blob-', 'r-cran-brio-', 'r-cran-cachem-', 'r-cran-callr-', 'r-cran-cli-', 'r-cran-codetools-', 'r-cran-colorspace-', 'r-cran-cpp11-', 'r-cran-crayon-', 'r-cran-curl-', 'r-cran-data.table-', 'r-cran-dbi-', 'r-cran-dbplyr-', 'r-cran-desc-', 'r-cran-diffobj-', 'r-cran-digest-', 'r-cran-dplyr-', 'r-cran-ellipsis-', 'r-cran-evaluate-', 'r-cran-fansi-', 'r-cran-farver-', 'r-cran-fastmap-', 'r-cran-filelock-', 'r-cran-formatr-', 'r-cran-fs-', 'r-cran-futile.logger-', 'r-cran-futile.options-', 'r-cran-generics-', 'r-cran-ggplot2-', 'r-cran-glue-', 'r-cran-gridextra-', 'r-cran-gtable-', 'r-cran-hms-', 'r-cran-httr-', 'r-cran-isoband-', 'r-cran-jsonlite-', 'r-cran-labeling-', 'r-cran-lambda.r-', 'r-cran-lattice-', 'r-cran-lifecycle-', 'r-cran-littler-', 'r-cran-magrittr-', 'r-cran-mass-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'r-cran-mclust-', 'r-cran-memoise-', 'r-cran-mgcv-', 'r-cran-mime-', 'r-cran-munsell-', 'r-cran-nlme-', 'r-cran-openssl-', 'r-cran-pillar-', 'r-cran-pkgbuild-', 'r-cran-pkgconfig-', 'r-cran-pkgkitten-', 'r-cran-pkgload-', 'r-cran-plogr-', 'r-cran-png-', 'r-cran-praise-', 'r-cran-prettyunits-', 'r-cran-processx-', 'r-cran-progress-', 'r-cran-ps-', 'r-cran-purrr-', 'r-cran-r6-', 'r-cran-rappdirs-', 'r-cran-rcolorbrewer-', 'r-cran-rcpp-', 'r-cran-rcurl-', 'r-cran-rematch2-', 'r-cran-restfulr-', 'r-cran-rjson-', 'r-cran-rlang-', 'r-cran-rprojroot-', 'r-cran-rsqlite-', 'r-cran-rstudioapi-', 'r-cran-scales-', 'r-cran-snow-', 'r-cran-stringi-', 'r-cran-stringr-', 'r-cran-sys-', 'r-cran-testthat-', 'r-cran-tibble-', 'r-cran-tidyr-', 'r-cran-tidyselect-', 'r-cran-utf8-', 'r-cran-vctrs-', 'r-cran-vgam-', 'r-cran-viridislite-', 'r-cran-waldo-', 'r-cran-withr-', 'r-cran-xml-', 'r-cran-xml2-', 'r-cran-yaml-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-purecn-'] 3m37.5s 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 gcc-11-base gcc-13-base hdf5-helpers libaec-dev libaec0 libasan6 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4-openssl-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-12-dev libgcc-13-dev libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libhwasan0 libice6 libicu67 libicu72 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery liblapack3 libldap-2.4-2 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsnappy1v5 libssh2-1t64 libssl-dev libstdc++-10-dev libstdc++-12-dev libstdc++-13-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff5 libtiff6 libtirpc-dev libtirpc3t64 libtk8.6 libtsan0 libtsan2 libubsan1 libuv1 libwebp6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv openssl 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-dnacopy 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-purecn r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-brio r-cran-cachem r-cran-callr r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gridextra r-cran-gtable r-cran-hms r-cran-httr r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mclust r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-png r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-rematch2 r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rprojroot r-cran-rsqlite r-cran-rstudioapi r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev The following NEW packages will be installed: libtirpc3 0 upgraded, 1 newly installed, 261 to remove and 0 not upgraded. Need to get 82.1 kB of archives. After this operation, 785 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 82.1 kB in 0s (1926 kB/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 ... 48626 files and directories currently installed.) Removing r-bioc-purecn (2.8.1+dfsg-1) ... Removing r-cran-ggplot2 (3.4.4+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-bioc-variantannotation (1.48.1-1) ... Removing r-bioc-genomicfeatures (1.54.3+dfsg-1) ... Removing r-bioc-bsgenome (1.70.2-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing libstdc++-10-dev:amd64 (10.5.0-3) ... Removing libgcc-10-dev:amd64 (10.5.0-3) ... Removing libtsan0:amd64 (11.4.0-7) ... Removing libasan6:amd64 (11.4.0-7) ... Removing gcc-11-base:amd64 (11.4.0-7) ... Removing r-bioc-rhdf5 (2.46.1+dfsg-1) ... Removing r-bioc-rhdf5filters (1.14.1+dfsg-3) ... Removing r-bioc-rhdf5lib (1.24.2+dfsg-1) ... Removing libhdf5-dev (1.10.10+repack-3.1) ... Removing hdf5-helpers (1.10.10+repack-3.1) ... Removing libaec-dev:amd64 (1.1.2-1) ... Removing libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.1) ... Removing libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.1) ... Removing libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1) ... Removing libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.1) ... Removing libstdc++-12-dev:amd64 (12.3.0-15) ... Removing libgcc-12-dev:amd64 (12.3.0-15) ... Removing r-cran-mclust (6.0.1-1) ... Removing libblosc1:amd64 (1.21.5+ds-1+b1) ... Removing r-bioc-biomart (2.58.2+dfsg-1) ... Removing r-bioc-annotationdbi (1.64.1-1) ... Removing r-bioc-keggrest (1.42.0+dfsg-1) ... Removing libjpeg-dev:amd64 (1:2.1.5-2+b2) ... Removing libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) ... Removing libcurl4-openssl-dev:amd64 (8.6.0-3.2) ... Removing r-bioc-biocfilecache (2.10.1+dfsg-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing r-bioc-dnacopy (1.76.0-1) ... Removing r-cran-data.table (1.14.10+dfsg-1) ... Removing libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.1) ... Removing libicu67:amd64 (67.1-7) ... 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 libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libnsl-dev:amd64 (1.3.0-3) ... Removing r-cran-png (0.1-8-1) ... Removing libsnappy1v5:amd64 (1.1.10-1+b1) ... Removing libssl-dev:amd64 (3.1.5-1.1) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Removing r-bioc-rtracklayer (1.62.0-1) ... Removing r-bioc-genomicalignments (1.38.2-1) ... Removing r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... Removing r-bioc-delayedarray (0.28.0+dfsg-1) ... Removing r-bioc-sparsearray (1.2.4+dfsg-1) ... Removing r-bioc-s4arrays (1.2.0+dfsg-1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-bioc-rsamtools (2.18.0+dfsg-1) ... Removing r-bioc-biocparallel (1.36.0-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-2.1) ... Removing libstdc++-13-dev:amd64 (13.2.0-18) ... Removing libgcc-13-dev:amd64 (13.2.0-18) ... Removing gcc-13-base:amd64 (13.2.0-18) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-3.1) ... Removing libsz2:amd64 (1.1.2-1) ... Removing libaec0:amd64 (1.1.2-1) ... Removing libasan8:amd64 (14-20240303-1) ... Removing libatomic1:amd64 (14-20240303-1) ... Removing r-bioc-rhtslib (2.4.1+dfsg-3) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-curl (5.2.0+dfsg-1) ... Removing r-bioc-biostrings (2.70.2+dfsg-1) ... Removing r-bioc-genomicranges (1.54.1+dfsg-1) ... Removing r-bioc-xvector (0.42.0-1) ... Removing r-bioc-zlibbioc (1.48.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libc6-dev:amd64 (2.37-15.1) ... Removing libc-dev-bin (2.37-15.1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... Removing libhwasan0:amd64 (14-20240303-1) ... Removing libitm1:amd64 (14-20240303-1) ... Removing liblsan0:amd64 (14-20240303-1) ... Removing libquadmath0:amd64 (14-20240303-1) ... dpkg: libwebp7:amd64: dependency problems, but removing anyway as you requested: libtiff6:amd64 depends on libwebp7 (>= 1.3.2). Removing libwebp7:amd64 (1.3.2-0.4) ... Removing libsharpyuv0:amd64 (1.3.2-0.4) ... dpkg: libssh2-1t64:amd64: dependency problems, but removing anyway as you requested: libcurl4t64:amd64 depends on libssh2-1t64 (>= 1.11.0). Removing libssh2-1t64:amd64 (1.11.0-4.1) ... dpkg: libtcl8.6:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libtcl8.6 (>= 8.6.0). libtk8.6:amd64 depends on libtcl8.6 (>= 8.6.0-2). Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... dpkg: libthai-data: dependency problems, but removing anyway as you requested: libthai0:amd64 depends on libthai-data (>= 0.1.10). Removing libthai-data (0.1.29-2) ... dpkg: libtirpc3t64:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libtirpc3 (>= 1.0.2); however: Package libtirpc3 is not installed. Package libtirpc3t64:amd64 which provides libtirpc3 is to be removed. libnsl2:amd64 depends on libtirpc3 (>= 1.0.2); however: Package libtirpc3 is not installed. Package libtirpc3t64:amd64 which provides libtirpc3 is to be removed. Removing libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' dpkg: r-base-core: dependency problems, but removing anyway as you requested: r-cran-viridislite depends on r-base-core (>= 4.3.1-1). r-cran-viridislite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tidyselect depends on r-base-core (>= 4.2.1-2). r-cran-tidyselect depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-sys depends on r-base-core (>= 4.3.1-1). r-cran-sys depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rjson depends on r-base-core (>= 4.1.2-1). r-cran-rjson depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-restfulr depends on r-base-core (>= 4.2.1-1). r-cran-restfulr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rematch2 depends on r-base-core (>= 4.0.0-3). r-cran-rematch2 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rappdirs depends on r-base-core (>= 4.0.3-1). r-cran-rappdirs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-praise depends on r-base-core (>= 4.0.0-3). r-cran-praise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-plogr depends on r-base-core (>= 4.0.0-3). r-cran-plogr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgkitten depends on r-base-core (>= 4.2.2.20221110-2). r-cran-pkgkitten depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-munsell depends on r-base-core (>= 4.0.0-3). r-cran-munsell depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mime depends on r-base-core (>= 4.2.1-2). r-cran-mime depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-memoise depends on r-base-core (>= 4.1.2-1). r-cran-memoise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-littler depends on r-base-core (>= 4.3.2-1). r-cran-littler depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lambda.r depends on r-base-core (>= 4.0.0-3). r-cran-lambda.r depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-isoband depends on r-base-core (>= 4.2.2.20221110-1). r-cran-isoband depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-hms depends on r-base-core (>= 4.3.1-1). r-cran-hms depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-gridextra depends on r-base-core (>= 4.0.0-3). r-cran-gridextra depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-generics depends on r-base-core (>= 4.2.1-1). r-cran-generics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.options depends on r-base-core (>= 4.0.0-3). r-cran-futile.options depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.logger depends on r-base-core (>= 4.0.0-3). r-cran-futile.logger depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-formatr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-formatr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fastmap depends on r-base-core (>= 4.2.2.20221110-2). r-cran-fastmap depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-farver depends on r-base-core (>= 4.2.1-1). r-cran-farver depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-diffobj depends on r-base-core (>= 4.2.1-2). r-cran-diffobj depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-colorspace depends on r-base-core (>= 4.2.2.20221110-2). r-cran-colorspace depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-codetools depends on r-base-core (>= 4.2.2.20221110-2). r-cran-codetools depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-callr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-callr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cachem depends on r-base-core (>= 4.3.0-1). r-cran-cachem depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-blob depends on r-base-core (>= 4.3.0-1). r-cran-blob depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bitops depends on r-base-core (>= 4.1.1-2). r-cran-bitops depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit64 depends on r-base-core (>= 4.0.2-1). r-cran-bit64 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit depends on r-base-core (>= 4.2.2.20221110-1). r-cran-bit depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-yaml depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-xml depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-withr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-waldo depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-viridislite depends on r-base-core (>= 4.3.1-1). r-cran-viridislite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-vgam depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-vctrs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-utf8 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tidyselect depends on r-base-core (>= 4.2.1-2). r-cran-tidyselect depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-testthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-sys depends on r-base-core (>= 4.3.1-1). r-cran-sys depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rstudioapi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rsqlite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rprojroot depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rlang depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rjson depends on r-base-core (>= 4.1.2-1). r-cran-rjson depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-restfulr depends on r-base-core (>= 4.2.1-1). r-cran-restfulr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rematch2 depends on r-base-core (>= 4.0.0-3). r-cran-rematch2 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rcurl depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rcpp depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rappdirs depends on r-base-core (>= 4.0.3-1). r-cran-rappdirs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-purrr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ps depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-progress depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-processx depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-prettyunits depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-praise depends on r-base-core (>= 4.0.0-3). r-cran-praise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-plogr depends on r-base-core (>= 4.0.0-3). r-cran-plogr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgload depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgkitten depends on r-base-core (>= 4.2.2.20221110-2). r-cran-pkgkitten depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgbuild depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-openssl depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-nlme depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-munsell depends on r-base-core (>= 4.0.0-3). r-cran-munsell depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mime depends on r-base-core (>= 4.2.1-2). r-cran-mime depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-memoise depends on r-base-core (>= 4.1.2-1). r-cran-memoise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-matrixstats depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mass depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-littler depends on r-base-core (>= 4.3.2-1). r-cran-littler depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lifecycle depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lattice depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lambda.r depends on r-base-core (>= 4.0.0-3). r-cran-lambda.r depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-labeling depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-jsonlite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-isoband depends on r-base-core (>= 4.2.2.20221110-1). r-cran-isoband depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-hms depends on r-base-core (>= 4.3.1-1). r-cran-hms depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-gtable depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-gridextra depends on r-base-core (>= 4.0.0-3). r-cran-gridextra depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-glue depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-generics depends on r-base-core (>= 4.2.1-1). r-cran-generics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.options depends on r-base-core (>= 4.0.0-3). r-cran-futile.options depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.logger depends on r-base-core (>= 4.0.0-3). r-cran-futile.logger depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-formatr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-formatr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-filelock depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fastmap depends on r-base-core (>= 4.2.2.20221110-2). r-cran-fastmap depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-farver depends on r-base-core (>= 4.2.1-1). r-cran-farver depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fansi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-evaluate depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-dplyr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-digest depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-diffobj depends on r-base-core (>= 4.2.1-2). r-cran-diffobj depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-desc depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-dbi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cpp11 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-colorspace depends on r-base-core (>= 4.2.2.20221110-2). r-cran-colorspace depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-codetools depends on r-base-core (>= 4.2.2.20221110-2). r-cran-codetools depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cli depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-callr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-callr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cachem depends on r-base-core (>= 4.3.0-1). r-cran-cachem depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-brio depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-blob depends on r-base-core (>= 4.3.0-1). r-cran-blob depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bitops depends on r-base-core (>= 4.1.1-2). r-cran-bitops depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit64 depends on r-base-core (>= 4.0.2-1). r-cran-bit64 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit depends on r-base-core (>= 4.2.2.20221110-1). r-cran-bit depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-askpass depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-s4vectors depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-matrixgenerics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-iranges depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-genomeinfodbdata depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-genomeinfodb depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biocio depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biocgenerics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biobase depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. Removing r-base-core (4.3.3-2) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.52.0+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.0+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.0+ds-1) ... Removing fontconfig (2.15.0-1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing libfontconfig1:amd64 (2.15.0-1) ... Removing fontconfig-config (2.15.0-1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... dpkg: libcurl4t64:amd64: dependency problems, but removing anyway as you requested: r-cran-rcurl depends on libcurl4 (>= 7.16.2); however: Package libcurl4 is not installed. Package libcurl4t64:amd64 which provides libcurl4 is to be removed. Removing libcurl4t64:amd64 (8.6.0-3.2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libxss1:amd64 (1:1.2.3-1) ... dpkg: libx11-6:amd64: dependency problems, but removing anyway as you requested: libxrender1:amd64 depends on libx11-6 (>= 2:1.6.0). libxext6:amd64 depends on libx11-6 (>= 2:1.6.0). Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... dpkg: libxcb1:amd64: dependency problems, but removing anyway as you requested: libxcb-render0:amd64 depends on libxcb1 (>= 1.8). Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.12.1-1) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libexpat1:amd64 (2.6.0-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libgfortran5:amd64 (14-20240303-1) ... Removing libglib2.0-0t64:amd64 (2.78.4-3) ... Removing libgomp1:amd64 (14-20240303-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... dpkg: libxml2:amd64: dependency problems, but removing anyway as you requested: r-cran-xml depends on libxml2 (>= 2.7.4). Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-3.1) ... 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+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libtirpc3: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 ... 21281 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.4+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.4+ds-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 ... 21288 files and directories currently installed.) Removing libtsan2:amd64 (14-20240303-1) ... Removing libubsan1:amd64 (14-20240303-1) ... Removing r-cran-testthat (3.2.1-1) ... Removing r-cran-pkgload (1.3.4-1) ... Removing r-cran-fs (1.6.3+dfsg-1) ... Removing libuv1:amd64 (1.48.0-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.16.1-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing linux-libc-dev (6.7.7-1) ... Removing r-cran-rcpp (1.0.12-1) ... Removing littler (0.3.19-1) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing openssl (3.1.5-1.1) ... Removing r-bioc-biobase (2.62.0-1) ... Removing r-bioc-genomeinfodb (1.38.6+dfsg-1) ... Removing r-bioc-iranges (2.36.0-1) ... Removing r-bioc-biocio (1.12.0+dfsg-1) ... Removing r-bioc-s4vectors (0.40.2+dfsg-1) ... Removing r-bioc-matrixgenerics (1.14.0-1) ... Removing r-bioc-biocgenerics (0.48.1-2) ... Removing r-bioc-genomeinfodbdata (1.2.11-2) ... Removing r-cran-openssl (2.1.1+dfsg-2) ... Removing r-cran-askpass (1.2.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-rsqlite (2.3.4-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-rcurl (1.98-1.14+dfsg-1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-brio (1.1.4-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.8-1) ... Removing r-cran-pkgbuild (1.4.3-1) ... Removing r-cran-callr (3.7.3-2) ... Removing r-cran-waldo (0.5.2-1) ... Removing r-cran-dplyr (1.1.4-1) ... Removing r-cran-tidyselect (1.2.0+dfsg-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-cpp11 (0.4.7-1) ... Removing r-cran-diffobj (0.3.5-1+b1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-dbi (1.2.2-1) ... Removing r-cran-desc (1.4.3-1) ... Removing r-cran-digest (0.6.34-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-evaluate (0.23-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-1) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-gtable (0.3.4+dfsg-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.164-1) ... Removing r-cran-lattice (0.22-5-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-littler (0.3.19-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-matrixstats (1.2.0-1) ... Removing r-cran-mime (0.12-1+b1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-processx (3.8.3-1) ... Removing r-cran-ps (1.7.6-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-rprojroot (2.0.4-1) ... Removing r-cran-rstudioapi (0.15.0-1) ... Removing r-cran-sys (3.4.2-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-vgam (1.1-9-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing r-cran-yaml (2.3.8-1) ... Removing readline-common (8.2-3.1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing r-cran-cli (3.6.2-1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 3m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libtirpc3:amd64=1.3.4+ds-1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'gcc-11-base:amd64-', 'gcc-13-base:amd64-', 'hdf5-helpers-', 'libaec-dev:amd64-', 'libaec0:amd64-', 'libasan6:amd64-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libblas3:amd64-', 'libblosc1:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4-openssl-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-13-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-cpp-103-1t64:amd64-', 'libhdf5-dev-', 'libhdf5-fortran-102t64:amd64-', 'libhdf5-hl-100t64:amd64-', 'libhdf5-hl-cpp-100t64:amd64-', 'libhdf5-hl-fortran-100t64:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libitm1:amd64-', 'libjbig0:amd64-', 'libjpeg-dev:amd64-', 'libjpeg62-turbo:amd64-', 'libjpeg62-turbo-dev:amd64-', 'libjs-jquery-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblsan0: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-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsnappy1v5:amd64-', 'libssh2-1t64:amd64-', 'libssl-dev:amd64-', 'libstdc++-10-dev:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libtsan0:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libuv1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'littler-', 'node-html5shiv-', 'openssl-', '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-dnacopy-', '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-rhdf5-', 'r-bioc-rhdf5filters-', 'r-bioc-rhdf5lib-', 'r-bioc-rhtslib-', 'r-bioc-rsamtools-', 'r-bioc-rtracklayer-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-summarizedexperiment-', 'r-bioc-variantannotation-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-askpass-', 'r-cran-assertthat-', 'r-cran-bh-', 'r-cran-bit-', 'r-cran-bit64-', 'r-cran-bitops-', 'r-cran-blob-', 'r-cran-brio-', 'r-cran-cachem-', 'r-cran-callr-', 'r-cran-cli-', 'r-cran-codetools-', 'r-cran-colorspace-', 'r-cran-cpp11-', 'r-cran-crayon-', 'r-cran-curl-', 'r-cran-data.table-', 'r-cran-dbi-', 'r-cran-dbplyr-', 'r-cran-desc-', 'r-cran-diffobj-', 'r-cran-digest-', 'r-cran-dplyr-', 'r-cran-ellipsis-', 'r-cran-evaluate-', 'r-cran-fansi-', 'r-cran-farver-', 'r-cran-fastmap-', 'r-cran-filelock-', 'r-cran-formatr-', 'r-cran-fs-', 'r-cran-futile.logger-', 'r-cran-futile.options-', 'r-cran-generics-', 'r-cran-ggplot2-', 'r-cran-glue-', 'r-cran-gridextra-', 'r-cran-gtable-', 'r-cran-hms-', 'r-cran-httr-', 'r-cran-isoband-', 'r-cran-jsonlite-', 'r-cran-labeling-', 'r-cran-lambda.r-', 'r-cran-lattice-', 'r-cran-lifecycle-', 'r-cran-littler-', 'r-cran-magrittr-', 'r-cran-mass-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'r-cran-mclust-', 'r-cran-memoise-', 'r-cran-mgcv-', 'r-cran-mime-', 'r-cran-munsell-', 'r-cran-nlme-', 'r-cran-openssl-', 'r-cran-pillar-', 'r-cran-pkgbuild-', 'r-cran-pkgconfig-', 'r-cran-pkgkitten-', 'r-cran-pkgload-', 'r-cran-plogr-', 'r-cran-png-', 'r-cran-praise-', 'r-cran-prettyunits-', 'r-cran-processx-', 'r-cran-progress-', 'r-cran-ps-', 'r-cran-purrr-', 'r-cran-r6-', 'r-cran-rappdirs-', 'r-cran-rcolorbrewer-', 'r-cran-rcpp-', 'r-cran-rcurl-', 'r-cran-rematch2-', 'r-cran-restfulr-', 'r-cran-rjson-', 'r-cran-rlang-', 'r-cran-rprojroot-', 'r-cran-rsqlite-', 'r-cran-rstudioapi-', 'r-cran-scales-', 'r-cran-snow-', 'r-cran-stringi-', 'r-cran-stringr-', 'r-cran-sys-', 'r-cran-testthat-', 'r-cran-tibble-', 'r-cran-tidyr-', 'r-cran-tidyselect-', 'r-cran-utf8-', 'r-cran-vctrs-', 'r-cran-vgam-', 'r-cran-viridislite-', 'r-cran-waldo-', 'r-cran-withr-', 'r-cran-xml-', 'r-cran-xml2-', 'r-cran-yaml-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-purecn-'] 3m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libtirpc3:amd64=1.3.4+ds-1'] 3m38.6s DUMP: Reading package lists... Building dependency tree... Reading state information... 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. debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/82.1 kB of archives. After this operation, 0 B of additional disk space will be used. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9463 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.4+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.4+ds-1) over (1.3.4+ds-1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-15.1) ... 3m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libtirpc3:amd64=1.3.4+ds-1'] 3m38.6s INFO: Running scripts post_remove 3m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_remove_exceptions'] 3m38.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_remove_exceptions'] 3m38.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4-openssl-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-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-dev', 'libhdf5-fortran-102t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhdf5-hl-cpp-100t64:amd64', 'libhdf5-hl-fortran-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0: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', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libssl-dev:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'openssl', '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-dnacopy', '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-rhdf5', 'r-bioc-rhdf5filters', 'r-bioc-rhdf5lib', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hms', 'r-cran-httr', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-rematch2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 3m39.3s DUMP: (Reading database ... 9463 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) ... Purging configuration files for fontconfig-config (2.15.0-1) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: ignoring request to remove gcc-11-base which isn't installed dpkg: warning: ignoring request to remove gcc-13-base which isn't installed dpkg: warning: ignoring request to remove hdf5-helpers which isn't installed dpkg: warning: ignoring request to remove libaec-dev which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libasan6 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libblosc1 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 libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-4) ... dpkg: warning: ignoring request to remove libcurl4-openssl-dev which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove 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-13-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-3) ... 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 libhdf5-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-dev which isn't installed dpkg: warning: ignoring request to remove libhdf5-fortran-102t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-cpp-100t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-fortran-100t64 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 libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg-dev which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo-dev which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove liblapack3 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 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) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-3.1) ... 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 libsnappy1v5 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libssl-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-10-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-dev which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.1) ... 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 libuv1 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 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 libxml2 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 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-html5shiv which isn't installed Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for r-base-core (4.3.3-2) ... dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocfilecache which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biomart which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-dnacopy 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-rhdf5 which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhdf5filters which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhdf5lib 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-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-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-brio which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-callr which isn't installed dpkg: warning: ignoring request to remove r-cran-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-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-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-desc which isn't installed dpkg: warning: ignoring request to remove r-cran-diffobj which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-gridextra which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-isoband which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-mclust which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgbuild which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgload which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-praise which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-processx which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-ps which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-rematch2 which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rprojroot which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-rstudioapi which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-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-testthat which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-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-vgam which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-waldo which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-3.1) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 3m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4-openssl-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-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-dev', 'libhdf5-fortran-102t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhdf5-hl-cpp-100t64:amd64', 'libhdf5-hl-fortran-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0: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', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libssl-dev:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'openssl', '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-dnacopy', '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-rhdf5', 'r-bioc-rhdf5filters', 'r-bioc-rhdf5lib', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-brio', 'r-cran-cachem', 'r-cran-callr', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gridextra', 'r-cran-gtable', 'r-cran-hms', 'r-cran-httr', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-plogr', 'r-cran-png', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-rematch2', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rsqlite', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 3m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', 'r-bioc-purecn'] 3m39.4s DUMP: dpkg: warning: ignoring request to remove r-bioc-purecn which isn't installed 3m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', 'r-bioc-purecn'] 3m39.4s INFO: Running scripts post_purge 3m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_purge_exceptions'] 3m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_purge_exceptions'] 3m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', '--pending'] 3m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--purge', '--pending'] 3m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--remove', '--pending'] 3m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg', '--remove', '--pending'] 3m39.4s INFO: Running scripts post_test 3m39.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_test_exceptions'] 3m39.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'tmp/scripts/post_test_exceptions'] 3m39.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m39.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-divert', '--list'] 3m39.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 3m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'dpkg-divert', '--list'] 3m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'clean'] 3m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpwrw8viat', 'apt-get', 'clean'] 3m40.0s DEBUG: Recording chroot state 3m40.6s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: 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 3m41.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/shm'] 3m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/shm'] 3m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/console'] 3m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/console'] 3m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/ptmx'] 3m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/ptmx'] 3m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/pts'] 3m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/dev/pts'] 3m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/proc'] 3m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpwrw8viat/proc'] 3m41.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m41.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpwrw8viat'] 3m41.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpwrw8viat 3m41.4s INFO: PASS: Upgrading between Debian distributions. 3m41.4s INFO: PASS: All tests. 3m41.4s INFO: piuparts run ends. ret=0 End: 2024-03-05 11:48:16 GMT