Start: 2024-08-22 15:58:02 GMT [bookworm] 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 [bookworm-next] 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 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt r-bioc-purecn=2.4.0+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 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt r-bioc-purecn=2.4.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpf85h8nu1 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpf85h8nu1 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpf85h8nu1/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'update'] 0m2.1s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s INFO: Running scripts post_setup 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m4.7s INFO: Running scripts is_testable 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/is_testable_uninstallable'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/is_testable_uninstallable'] 0m4.7s INFO: Running scripts pre_test 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_test_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_test_root_password'] 0m4.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_test_root_password'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m4.9s 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 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m4.9s INFO: apt-cache knows about the following packages: r-bioc-purecn 0m4.9s INFO: Running scripts pre_install 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m5.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m5.0s DUMP: r-bioc-purecn: Installed: (none) Candidate: 2.4.0+dfsg-1 Version table: 2.4.0+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m39.5s 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 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libcurl4-openssl-dev libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 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 libice6 libicu72 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 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 libssl-dev libssl3 libstdc++-12-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 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-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-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock 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-mclust r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite 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 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 libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config low-memory-monitor krb5-doc krb5-user libhdf5-doc libssl-doc libstdc++-12-doc tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-go.db r-cran-runit r-bioc-org.hs.eg.db r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-testthat r-cran-rmarkdown r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-shortread r-cran-batchtools r-cran-mockery r-cran-webmockr r-cran-biocmanager r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-edger r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-cran-pscbs r-cran-r.utils r-cran-covr r-cran-optparse r-cran-tinytest r-bioc-limma r-bioc-snpstats r-cran-roxygen2 r-cran-ff r-cran-callr r-cran-htmltools r-cran-htmlwidgets r-cran-processx r-cran-ps r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-jpeg r-cran-viridis r-cran-bench r-cran-desc r-cran-spelling r-cran-xts r-cran-nanotime r-cran-zoo r-cran-rmysql r-cran-unitizer r-cran-profvis r-cran-rgeos r-cran-forcats r-cran-waldo r-cran-lubridate r-cran-httpuv r-cran-readr r-cran-magick r-cran-sf r-cran-r.rsp r-cran-lintr r-cran-tidyverse r-cran-getopt r-cran-base64enc r-cran-r.devices r-cran-geometry r-cran-formattable r-cran-palmerpenguins r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline r-cran-fs r-cran-usethis r-cran-gert r-cran-gh r-cran-rvest r-cran-dichromat r-cran-rlecuyer r-cran-brio r-cran-evaluate r-cran-pkgbuild r-cran-pkgload r-cran-tidyr r-cran-pkgdown r-cran-zeallot readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-bioc-biovizbase r-cran-knitr r-cran-rmarkdown r-bioc-biocstyle r-cran-testthat r-cran-mockery r-cran-decor r-cran-brio r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-bench r-cran-broom r-cran-callr r-cran-covr r-cran-lobstr r-cran-testit r-cran-survival r-cran-pkgload r-cran-ragg r-cran-hexbin r-cran-hmisc r-cran-interp r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-sp r-cran-runit r-cran-sodium r-cran-lubridate r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets r-cran-mockr r-cran-formattable r-cran-waldo libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core hdf5-helpers libaec-dev libaec0 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libcurl4-openssl-dev libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 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 libice6 libicu72 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 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 libssl-dev libssl3 libstdc++-12-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 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-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-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock 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-mclust r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite 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 0 upgraded, 233 newly installed, 0 to remove and 0 not upgraded. Need to get 235 MB of archives. After this operation, 620 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:18 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:21 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libblosc1 amd64 1.21.3+ds-1 [49.3 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:37 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u7 [1899 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:49 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-10+deb12u6 [491 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.13-1~deb12u1 [2435 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:103 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:117 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:151 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:155 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:158 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:183 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 r-bioc-bsgenome all 1.66.3-1 [6997 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 r-bioc-dnacopy amd64 1.72.3-1 [377 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 r-bioc-variantannotation amd64 1.44.1-1 [3642 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 r-cran-data.table amd64 1.14.8+dfsg-1 [1683 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-cran-gridextra all 2.3-3 [1024 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 r-cran-vgam amd64 1.1-7-1 [7230 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 r-cran-mclust amd64 6.0.0-1 [3945 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5lib amd64 1.20.0+dfsg-1 [102 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5filters amd64 1.10.0+dfsg-1 [120 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5 amd64 2.42.0+dfsg-1 [792 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-bioc-purecn all 2.4.0+dfsg-1 [6025 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 235 MB in 2s (108 MB/s) Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6093 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../002-libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.13-1~deb12u1_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../006-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../008-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-libfreetype6_2.12.1+dfsg-5+deb12u3_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.14.1-4_amd64.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../014-hdf5-helpers_1.10.8+repack1-1_amd64.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../015-libaec0_1.0.6-1+b1_amd64.deb ... Unpacking libaec0:amd64 (1.0.6-1+b1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../016-libsz2_1.0.6-1+b1_amd64.deb ... Unpacking libsz2:amd64 (1.0.6-1+b1) ... Selecting previously unselected package libaec-dev:amd64. Preparing to unpack .../017-libaec-dev_1.0.6-1+b1_amd64.deb ... Unpacking libaec-dev:amd64 (1.0.6-1+b1) ... Selecting previously unselected package libasan8:amd64. Preparing to unpack .../018-libasan8_12.2.0-14_amd64.deb ... Unpacking libasan8:amd64 (12.2.0-14) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../019-libatomic1_12.2.0-14_amd64.deb ... Unpacking libatomic1:amd64 (12.2.0-14) ... 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Unpacking linux-libc-dev:amd64 (6.1.94-1) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../032-libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../033-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../034-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../035-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../036-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../037-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../038-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3:amd64. Preparing to unpack .../039-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../040-libnsl2_1.3.0-2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../041-libtirpc-dev_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../042-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../043-rpcsvc-proto_1.4.3-1_amd64.deb ... Unpacking rpcsvc-proto (1.4.3-1) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../044-libc6-dev_2.36-9+deb12u7_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u7) ... Selecting previously unselected package libstdc++-12-dev:amd64. Preparing to unpack .../045-libstdc++-12-dev_12.2.0-14_amd64.deb ... Unpacking libstdc++-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../046-libboost1.74-dev_1.74.0+ds1-21_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../047-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../048-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../049-libpixman-1-0_0.42.2-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../050-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../051-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../052-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../053-libx11-data_2%3a1.8.4-2+deb12u2_all.deb ... Unpacking libx11-data (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libx11-6:amd64. 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Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../060-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../061-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../062-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../063-libnghttp2-14_1.52.0-1+deb12u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../064-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../065-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../066-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../067-libcurl4_7.88.1-10+deb12u6_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-10+deb12u6) ... Selecting previously unselected package libcurl4-openssl-dev:amd64. Preparing to unpack .../068-libcurl4-openssl-dev_7.88.1-10+deb12u6_amd64.deb ... Unpacking libcurl4-openssl-dev:amd64 (7.88.1-10+deb12u6) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../069-libdatrie1_0.2.13-2+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-2+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../070-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../071-libfribidi0_1.0.8-2.1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.8-2.1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../072-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../073-libglib2.0-0_2.74.6-2+deb12u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../074-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../075-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libhdf5-103-1:amd64. 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Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-stringi (1.7.12-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Setting up r-cran-cpp11 (0.4.3-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-gridextra (2.3-3) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up r-bioc-dnacopy (1.72.3-1) ... Setting up r-cran-cachem (1.0.7-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up r-cran-rjson (0.2.21-1) ... Setting up r-cran-rcurl (1.98-1.10+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-openssl (2.0.5+dfsg-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up r-cran-stringr (1.5.0-1) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2) ... Setting up r-bioc-biocio (1.8.0+dfsg-1) ... Setting up r-bioc-zlibbioc (1.44.0+dfsg-1) ... Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... 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-cran-scales (1.2.1-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-blob (1.2.3-1) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up r-cran-dbplyr (2.3.0+dfsg-1) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-cran-bh (1.74.0-2) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up r-bioc-biocfilecache (2.6.1+dfsg-1) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-bioc-rhdf5lib (1.20.0+dfsg-1) ... Setting up r-bioc-rhdf5filters (1.10.0+dfsg-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-rhdf5 (2.42.0+dfsg-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+deb12u7) ... 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. 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m39.5s INFO: Running scripts post_install 0m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m39.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m41.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m41.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpf85h8nu1 to bookworm-next 0m41.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m41.5s INFO: Running scripts pre_distupgrade 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'update'] 0m42.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:3 http://security.debian.org bookworm-security InRelease [48.0 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [109 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [62.8 kB] Fetched 647 kB in 1s (1167 kB/s) Reading package lists... 0m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'update'] 0m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-yf', 'dist-upgrade'] 0m47.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl-dev libssl3 libsystemd0 libudev1 linux-libc-dev openssl 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 14.2 MB of archives. After this operation, 38.9 kB of additional disk space will be used. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6-dev amd64 2.36-9+deb12u8 [1900 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-dev-bin amd64 2.36-9+deb12u8 [46.3 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 linux-libc-dev amd64 6.1.106-2 [2027 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:11 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:12 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl-dev amd64 3.0.13-1~deb12u2 [2436 kB] Get:13 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.13-1~deb12u2 [2023 kB] Get:14 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.13-1~deb12u2 [1421 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.2 MB in 0s (114 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 ... 37999 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.36-9+deb12u8_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../libc-dev-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Preparing to unpack .../linux-libc-dev_6.1.106-2_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.106-2) over (6.1.94-1) ... Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37999 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37999 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37999 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37999 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl-dev_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl-dev:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-libssl3_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../6-openssl_3.0.13-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Setting up libssl3:amd64 (3.0.13-1~deb12u2) ... Setting up linux-libc-dev:amd64 (6.1.106-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libssl-dev:amd64 (3.0.13-1~deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up libc-dev-bin (2.36-9+deb12u8) ... Setting up openssl (3.0.13-1~deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u8) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-yf', 'dist-upgrade'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m47.6s DUMP: 0bdc56bc83ae6d8c6f994c42aef2be7c - 0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m47.9s 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 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-purecn'] 0m47.9s INFO: apt-cache knows about the following packages: r-bioc-purecn 0m47.9s INFO: Running scripts pre_install 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m48.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m48.1s 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 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m48.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-purecn is already the newest version (2.4.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn'] 0m48.4s INFO: Running scripts post_install 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m48.4s INFO: Running scripts post_distupgrade 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_exceptions'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_exceptions'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m48.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m48.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m48.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m50.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m50.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m51.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m51.6s INFO: Running scripts pre_install 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_database-server'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_exceptions'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_extras'] 0m51.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m51.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy'] 0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m51.8s 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 0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-cache', 'policy', 'r-bioc-purecn'] 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn=2.4.0+dfsg-1'] 0m52.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-purecn is already the newest version (2.4.0+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', '-y', 'install', 'r-bioc-purecn=2.4.0+dfsg-1'] 0m52.4s INFO: Running scripts post_install 0m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_install_exceptions'] 0m52.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m54.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 0m55.0s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m55.0s INFO: /bin converted to /usr/bin by /usr merge 0m55.0s INFO: /lib converted to /usr/lib by /usr merge 0m55.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m55.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m55.0s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m55.0s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m55.0s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m55.0s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m55.0s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m55.0s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m55.0s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m55.0s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m55.0s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m55.0s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m55.0s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m55.0s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m55.0s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m55.0s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m55.0s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m55.0s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m55.0s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m55.0s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m55.0s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m55.0s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m55.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m55.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m55.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m55.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m58.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', '-ac', '--ignore-obsolete'] 1m1.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', '-ac', '--ignore-obsolete'] 1m1.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m1.0s DUMP: 0.15.6 1m1.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m1.0s INFO: Running adequate version 0.15.6 now. 1m1.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'r-bioc-purecn'] 1m1.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'r-bioc-purecn'] 1m1.1s INFO: Running scripts pre_remove 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_exceptions'] 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/pre_remove_exceptions'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.2s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hdf5-helpers hdf5-helpers 1.10.8+repack1-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libaec-dev:amd64 libaec-dev 1.0.6-1+b1 install ok installed libaec0:amd64 libaec0 1.0.6-1+b1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libasan8:amd64 libasan8 12.2.0-14 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libblosc1:amd64 libblosc1 1.21.3+ds-1 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-21 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc-dev-bin libc-dev-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libc6-dev:amd64 libc6-dev 2.36-9+deb12u8 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.33-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u6 install ok installed libcurl4-openssl-dev:amd64 libcurl4-openssl-dev 7.88.1-10+deb12u6 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.2.0-14 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.8+repack1-1 install ok installed libhdf5-cpp-103-1:amd64 libhdf5-cpp-103-1 1.10.8+repack1-1 install ok installed libhdf5-dev libhdf5-dev 1.10.8+repack1-1 install ok installed libhdf5-fortran-102:amd64 libhdf5-fortran-102 1.10.8+repack1-1 install ok installed libhdf5-hl-100:amd64 libhdf5-hl-100 1.10.8+repack1-1 install ok installed libhdf5-hl-cpp-100:amd64 libhdf5-hl-cpp-100 1.10.8+repack1-1 install ok installed libhdf5-hl-fortran-100:amd64 libhdf5-hl-fortran-100 1.10.8+repack1-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libitm1:amd64 libitm1 12.2.0-14 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg-dev:amd64 libjpeg-dev 1:2.1.5-2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libjpeg62-turbo-dev:amd64 libjpeg62-turbo-dev 1:2.1.5-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblsan0:amd64 liblsan0 12.2.0-14 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.9-3 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl-dev:amd64 libssl-dev 3.0.13-1~deb12u2 install ok installed libssl3:amd64 libssl3 3.0.13-1~deb12u2 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.2.0-14 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libsz2:amd64 libsz2 1.0.6-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 12.2.0-14 install ok installed libubsan1:amd64 libubsan1 12.2.0-14 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed 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 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 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 libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.1.106-2 install ok installed littler littler 0.3.17-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed openssl openssl 3.0.13-1~deb12u2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed r-base-core r-base-core 4.2.2.20221110-2 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.60.0-1 install ok installed r-bioc-biobase r-bioc-biobase 2.58.0-2 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.6.1+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.44.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.8.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.32.5-1 install ok installed r-bioc-biomart r-bioc-biomart 2.54.0+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.66.0-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.66.3-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.24.0+dfsg-1 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.72.3-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.34.9-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.9-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.34.0-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.50.4+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.50.2+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.32.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.38.0+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.10.0-1 install ok installed r-bioc-purecn r-bioc-purecn 2.4.0+dfsg-1 install ok installed r-bioc-rhdf5 r-bioc-rhdf5 2.42.0+dfsg-1 install ok installed r-bioc-rhdf5filters r-bioc-rhdf5filters 1.10.0+dfsg-1 install ok installed r-bioc-rhdf5lib r-bioc-rhdf5lib 1.20.0+dfsg-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.14.0-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.58.0-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.36.1-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.28.0+dfsg-1 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.44.1-1 install ok installed r-bioc-xvector r-bioc-xvector 0.38.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.44.0+dfsg-1 install ok installed r-cran-askpass r-cran-askpass 1.1-2 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.74.0-2 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.3-1 install ok installed r-cran-cachem r-cran-cachem 1.0.7-1 install ok installed r-cran-cli r-cran-cli 3.6.0-1 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 0.4.3-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.0.0+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.14.8+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.1.3-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.3.0+dfsg-1 install ok installed r-cran-digest r-cran-digest 0.6.31-1 install ok installed r-cran-dplyr r-cran-dplyr 1.0.10-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-fansi r-cran-fansi 1.0.4-1 install ok installed r-cran-farver r-cran-farver 2.1.1-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-filelock r-cran-filelock 1.0.2-2 install ok installed r-cran-formatr r-cran-formatr 1.14-1 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 3.4.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.6.2-1 install ok installed r-cran-gridextra r-cran-gridextra 2.3-3 install ok installed r-cran-gtable r-cran-gtable 0.3.1+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.2-1 install ok installed r-cran-httr r-cran-httr 1.4.5+dfsg-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.4+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.20-45-3 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.3+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.17-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-58.2-1 install ok installed r-cran-matrix r-cran-matrix 1.5-3-1 install ok installed r-cran-matrixstats r-cran-matrixstats 0.63.0-1 install ok installed r-cran-mclust r-cran-mclust 6.0.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-41-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.162-1 install ok installed r-cran-openssl r-cran-openssl 2.0.5+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.8.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.2-2 install ok installed r-cran-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-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-progress r-cran-progress 1.2.2-2 install ok installed r-cran-purrr r-cran-purrr 1.0.1-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.10-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.10+dfsg-1 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 1.0.6-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.2.20-1 install ok installed r-cran-scales r-cran-scales 1.2.1-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-stringi r-cran-stringi 1.7.12-1 install ok installed r-cran-stringr r-cran-stringr 1.5.0-1 install ok installed r-cran-sys r-cran-sys 3.4.1-1 install ok installed r-cran-tibble r-cran-tibble 3.1.8+dfsg-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.5.2-1 install ok installed r-cran-vgam r-cran-vgam 1.1-7-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.1-1 install ok installed r-cran-withr r-cran-withr 2.5.0-1 install ok installed r-cran-xml r-cran-xml 3.99-0.13-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.3-1+b1 install ok installed r-cran-yaml r-cran-yaml 2.3.7-1 install ok installed readline-common readline-common 8.2-1.3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.13.dfsg-1 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libcurl4-openssl-dev:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-dev', 'libhdf5-fortran-102:amd64', 'libhdf5-hl-100:amd64', 'libhdf5-hl-cpp-100:amd64', 'libhdf5-hl-fortran-100:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', '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-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', '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-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', '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'] 1m10.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core hdf5-helpers libaec-dev libaec0 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libcurl4-openssl-dev libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 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 libice6 libicu72 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 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 libssl-dev libssl3 libstdc++-12-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 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-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-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock 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-mclust r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-scales r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-vgam r-cran-viridislite 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 0 upgraded, 0 newly installed, 233 to remove and 0 not upgraded. After this operation, 620 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37999 files and directories currently installed.) Removing r-bioc-purecn (2.4.0+dfsg-1) ... Removing r-bioc-variantannotation (1.44.1-1) ... Removing r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Removing r-bioc-biomart (2.54.0+dfsg-1) ... Removing r-bioc-biocfilecache (2.6.1+dfsg-1) ... Removing r-cran-ggplot2 (3.4.1+dfsg-1) ... Removing r-cran-scales (1.2.1-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-bioc-rhdf5 (2.42.0+dfsg-1) ... Removing r-bioc-rhdf5filters (1.10.0+dfsg-1) ... Removing r-bioc-rhdf5lib (1.20.0+dfsg-1) ... Removing libhdf5-dev (1.10.8+repack1-1) ... Removing hdf5-helpers (1.10.8+repack1-1) ... Removing libaec-dev:amd64 (1.0.6-1+b1) ... Removing libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1) ... Removing libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1) ... Removing libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Removing libhdf5-fortran-102:amd64 (1.10.8+repack1-1) ... Removing r-cran-mclust (6.0.0-1) ... Removing r-cran-mgcv (1.8-41-1) ... Removing libblosc1:amd64 (1.21.3+ds-1) ... Removing libcurl4-openssl-dev:amd64 (7.88.1-10+deb12u6) ... Removing r-bioc-annotationdbi (1.60.0-1) ... Removing r-bioc-keggrest (1.38.0+dfsg-1) ... Removing r-cran-httr (1.4.5+dfsg-1) ... Removing r-cran-curl (5.0.0+dfsg-1) ... Removing r-bioc-bsgenome (1.66.3-1) ... Removing libjpeg-dev:amd64 (1:2.1.5-2) ... Removing libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Removing r-bioc-dnacopy (1.72.3-1) ... Removing r-cran-data.table (1.14.8+dfsg-1) ... Removing libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ... Removing r-cran-stringr (1.5.0-1) ... Removing r-cran-stringi (1.7.12-1) ... Removing r-cran-xml2 (1.3.3-1+b1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing r-cran-png (0.1-8-1) ... Removing libsnappy1v5:amd64 (1.1.9-3) ... Removing libssl-dev:amd64 (3.0.13-1~deb12u2) ... Removing r-cran-openssl (2.0.5+dfsg-1) ... Removing littler (0.3.17-1) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing r-cran-askpass (1.1-2) ... Removing r-cran-dbplyr (2.3.0+dfsg-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-progress (1.2.2-2) ... Removing r-cran-hms (1.1.2-1) ... Removing r-cran-dplyr (1.0.10-1) ... Removing r-cran-tidyselect (1.2.0+dfsg-1) ... Removing r-cran-purrr (1.0.1-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.1-0+dfsg-1) ... Removing r-cran-digest (0.6.31-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-tibble (3.1.8+dfsg-1) ... Removing r-cran-pillar (1.8.1+dfsg-1) ... Removing r-cran-fansi (1.0.4-1) ... Removing r-cran-farver (2.1.1-1) ... Removing r-cran-filelock (1.0.2-2) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-gridextra (2.3-3) ... Removing r-cran-gtable (0.3.1+dfsg-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.4+dfsg-1) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-nlme (3.1.162-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-58.2-1) ... Removing r-cran-mime (0.12-1+b1) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sys (3.4.1-1) ... Removing r-cran-utf8 (1.2.3-1) ... Removing r-cran-vgam (1.1-7-1) ... Removing r-cran-viridislite (0.4.1-1) ... Removing r-cran-withr (2.5.0-1) ... Removing r-bioc-rtracklayer (1.58.0-1) ... Removing r-bioc-genomicalignments (1.34.0-1) ... Removing r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Removing r-bioc-delayedarray (0.24.0+dfsg-1) ... Removing r-cran-matrix (1.5-3-1) ... Removing r-cran-rsqlite (2.2.20-1) ... Removing r-cran-rcpp (1.0.10-1) ... Removing libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Removing libsz2:amd64 (1.0.6-1+b1) ... Removing libaec0:amd64 (1.0.6-1+b1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.13-1) ... Removing r-bioc-biobase (2.58.0-2) ... Removing r-bioc-biocio (1.8.0+dfsg-1) ... Removing r-bioc-matrixgenerics (1.10.0-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.3-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.7-1) ... Removing r-cran-vctrs (0.5.2-1) ... Removing r-cran-dbi (1.1.3-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-lifecycle (1.0.3+dfsg-1) ... Removing r-cran-glue (1.6.2-1) ... Removing r-cran-lattice (0.20-45-3) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-littler (0.3.17-1) ... Removing r-cran-matrixstats (0.63.0-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.2-2) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-rlang (1.0.6-1) ... Removing r-cran-yaml (2.3.7-1) ... Removing r-bioc-rsamtools (2.14.0-1) ... Removing r-bioc-biocparallel (1.32.5-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-bh (1.74.0-2) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Removing libstdc++-12-dev:amd64 (12.2.0-14) ... Removing libgcc-12-dev:amd64 (12.2.0-14) ... Removing libasan8:amd64 (12.2.0-14) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing r-bioc-genomicranges (1.50.2+dfsg-1) ... Removing r-bioc-rhtslib (2.0.0+dfsg-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libitm1:amd64 (12.2.0-14) ... Removing liblsan0:amd64 (12.2.0-14) ... Removing libtsan2:amd64 (12.2.0-14) ... Removing libubsan1:amd64 (12.2.0-14) ... Removing r-bioc-biostrings (2.66.0-1) ... Removing r-bioc-genomeinfodb (1.34.9-1) ... Removing r-bioc-genomeinfodbdata (1.2.9-1) ... Removing r-cran-rcurl (1.98-1.10+dfsg-1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-cli (3.6.0-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-cpp11 (0.4.3-1) ... Removing r-cran-crayon (1.5.2-1) ... 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-bioc-xvector (0.38.0-1) ... Removing r-bioc-zlibbioc (1.44.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Removing libc6-dev:amd64 (2.36-9+deb12u8) ... Removing libc-dev-bin (2.36-9+deb12u8) ... Removing libcrypt-dev:amd64 (1:4.4.33-2) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.3+ds-1) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing linux-libc-dev:amd64 (6.1.106-2) ... Removing r-bioc-iranges (2.32.0-1) ... Removing r-bioc-s4vectors (0.36.1-1) ... Removing r-bioc-biocgenerics (0.44.0-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-base-core (4.2.2.20221110-2) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpango-1.0-0:amd64 (1.50.12+ds-1) ... Removing fontconfig (2.14.1-4) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libcurl4:amd64 (7.88.1-10+deb12u6) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.29-1) ... Removing libdatrie1:amd64 (0.2.13-2+b1) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libicu72:amd64 (72.1-3) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing openssl (3.0.13-1~deb12u2) ... Removing libssl3:amd64 (3.0.13-1~deb12u2) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libthai-data (0.1.29-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing readline-common (8.2-1.3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.17+nmu1) ... 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 libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libcurl4-openssl-dev:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-dev', 'libhdf5-fortran-102:amd64', 'libhdf5-hl-100:amd64', 'libhdf5-hl-cpp-100:amd64', 'libhdf5-hl-fortran-100:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', '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-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', '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-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', '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'] 1m10.0s INFO: Running scripts post_remove 1m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_remove_exceptions'] 1m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_remove_exceptions'] 1m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libcurl4-openssl-dev:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-dev', 'libhdf5-fortran-102:amd64', 'libhdf5-hl-100:amd64', 'libhdf5-hl-cpp-100:amd64', 'libhdf5-hl-fortran-100:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', '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-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', '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-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', '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'] 1m10.7s DUMP: (Reading database ... 6140 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.14.1-4) ... Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... 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 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 libboost1.74-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 (1:4.4.33-2) ... dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libcurl4-openssl-dev 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-12-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103-1 which isn't installed dpkg: warning: ignoring request to remove libhdf5-dev which isn't installed dpkg: warning: ignoring request to remove libhdf5-fortran-102 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-cpp-100 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-fortran-100 which isn't installed dpkg: warning: ignoring request to remove libice6 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 libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 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 libnsl2 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 libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed 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 libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl-dev which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-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 libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 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 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 libxt6 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 (3.0.13-1~deb12u2) ... Purging configuration files for r-base-core (4.2.2.20221110-2) ... 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-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-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-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-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-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-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-rsqlite 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-tibble 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-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 (8.2-1.3) ... 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: 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 1m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libcurl4-openssl-dev:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-dev', 'libhdf5-fortran-102:amd64', 'libhdf5-hl-100:amd64', 'libhdf5-hl-cpp-100:amd64', 'libhdf5-hl-fortran-100:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', '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-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', '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-mclust', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-scales', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-vgam', 'r-cran-viridislite', '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'] 1m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', 'r-bioc-purecn'] 1m10.7s DUMP: dpkg: warning: ignoring request to remove r-bioc-purecn which isn't installed 1m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', 'r-bioc-purecn'] 1m10.7s INFO: Running scripts post_purge 1m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_purge_exceptions'] 1m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_purge_exceptions'] 1m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', '--pending'] 1m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--purge', '--pending'] 1m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--remove', '--pending'] 1m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg', '--remove', '--pending'] 1m10.8s INFO: Running scripts post_test 1m10.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_test_exceptions'] 1m10.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'tmp/scripts/post_test_exceptions'] 1m10.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 1m11.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 1m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-divert', '--list'] 1m11.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'dpkg-divert', '--list'] 1m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'clean'] 1m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1', 'apt-get', 'clean'] 1m11.3s DEBUG: Recording chroot state 1m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/shm'] 1m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/shm'] 1m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/console'] 1m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/console'] 1m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/ptmx'] 1m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/ptmx'] 1m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts'] 1m12.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/dev/pts'] 1m12.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/proc'] 1m12.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1/proc'] 1m12.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 1m12.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpf85h8nu1'] 1m12.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpf85h8nu1 1m12.7s INFO: PASS: Upgrading between Debian distributions. 1m12.7s INFO: PASS: All tests. 1m12.7s INFO: piuparts run ends. ret=0 End: 2024-08-22 15:59:15 GMT