Start: 2024-11-15 03:21:48 GMT [testing] Package: r-bioc-tcgabiolinks Version: 2.32.0+dfsg-2 Installed-Size: 6550 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-downloader (>= 0.4), r-bioc-biomart, r-cran-dplyr, r-cran-tibble, r-bioc-genomicranges, r-cran-xml (>= 3.98.0), r-cran-data.table, r-cran-jsonlite (>= 1.0.0), r-cran-plyr, r-cran-knitr, r-cran-ggplot2, r-cran-stringr (>= 1.0.0), r-bioc-iranges, r-cran-rvest (>= 0.3.0), r-bioc-s4vectors, r-cran-r.utils, r-bioc-summarizedexperiment (>= 1.4.0), r-bioc-tcgabiolinksgui.data (>= 1.15.1), r-cran-readr, r-cran-tidyr, r-cran-purrr, r-cran-xml2, r-cran-httr (>= 1.2.1) Suggests: r-cran-jpeg, r-cran-png, r-bioc-biocstyle, r-cran-rmarkdown, r-cran-devtools, r-cran-parmigene, r-bioc-biobase, r-bioc-affy, r-cran-testthat, r-bioc-annotationhub, r-bioc-experimenthub, r-cran-seurat, r-bioc-complexheatmap, r-cran-circlize, r-bioc-consensusclusterplus, r-cran-igraph, r-bioc-limma, r-bioc-edger, r-bioc-sva, r-bioc-edaseq, r-cran-survminer, r-bioc-genefilter, r-cran-gridextra, r-cran-survival, r-cran-doparallel, r-cran-ggrepel (>= 0.6.3), r-cran-scales, r-cran-dt Description: GNU R/Bioconductor package for integrative analysis with GDC data Homepage: https://bioconductor.org/packages/TCGAbiolinks/ Description-md5: a12bea649d7df136b7f6898c8a08d8c7 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tcgabiolinks/r-bioc-tcgabiolinks_2.32.0+dfsg-2_all.deb Size: 6299404 MD5sum: 3a1990425990ffd849e39807ad7d396a SHA256: 60256b7cf7f92972e6638e4215d9fe148baa6246aac2336222849fd401bdb705 [sid] Package: r-bioc-tcgabiolinks Version: 2.32.0+dfsg-2 Installed-Size: 6550 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-downloader (>= 0.4), r-bioc-biomart, r-cran-dplyr, r-cran-tibble, r-bioc-genomicranges, r-cran-xml (>= 3.98.0), r-cran-data.table, r-cran-jsonlite (>= 1.0.0), r-cran-plyr, r-cran-knitr, r-cran-ggplot2, r-cran-stringr (>= 1.0.0), r-bioc-iranges, r-cran-rvest (>= 0.3.0), r-bioc-s4vectors, r-cran-r.utils, r-bioc-summarizedexperiment (>= 1.4.0), r-bioc-tcgabiolinksgui.data (>= 1.15.1), r-cran-readr, r-cran-tidyr, r-cran-purrr, r-cran-xml2, r-cran-httr (>= 1.2.1) Suggests: r-cran-jpeg, r-cran-png, r-bioc-biocstyle, r-cran-rmarkdown, r-cran-devtools, r-cran-parmigene, r-bioc-biobase, r-bioc-affy, r-cran-testthat, r-bioc-annotationhub, r-bioc-experimenthub, r-cran-seurat, r-bioc-complexheatmap, r-cran-circlize, r-bioc-consensusclusterplus, r-cran-igraph, r-bioc-limma, r-bioc-edger, r-bioc-sva, r-bioc-edaseq, r-cran-survminer, r-bioc-genefilter, r-cran-gridextra, r-cran-survival, r-cran-doparallel, r-cran-ggrepel (>= 0.6.3), r-cran-scales, r-cran-dt Description: GNU R/Bioconductor package for integrative analysis with GDC data Homepage: https://bioconductor.org/packages/TCGAbiolinks/ Description-md5: a12bea649d7df136b7f6898c8a08d8c7 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tcgabiolinks/r-bioc-tcgabiolinks_2.32.0+dfsg-2_all.deb Size: 6299404 MD5sum: 3a1990425990ffd849e39807ad7d396a SHA256: 60256b7cf7f92972e6638e4215d9fe148baa6246aac2336222849fd401bdb705 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-tcgabiolinks=2.32.0+dfsg-2 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-tcgabiolinks=2.32.0+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpsr2gesox 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpsr2gesox 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/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/tmpsr2gesox/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/tmpsr2gesox/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpsr2gesox/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'update'] 0m2.2s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9356 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6252 kB] Fetched 15.8 MB in 1s (13.5 MB/s) Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-yf', 'dist-upgrade'] 0m4.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: gcc-14-base libaudit-common libaudit1 libcap-ng0 libdebconfclient0 libgcc-s1 libseccomp2 libselinux1 libsemanage2 libstdc++6 perl-base tzdata 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3075 kB of archives. After this operation, 6144 B disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.40.0-7 [1675 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:4.0.1-3 [12.4 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-3+b1 [17.5 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:4.0.1-3 [54.6 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-1+b3 [47.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.7-3+b1 [77.0 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3075 kB in 0s (52.3 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 ... 5167 files and directories currently installed.) Preparing to unpack .../perl-base_5.40.0-7_amd64.deb ... Unpacking perl-base (5.40.0-7) over (5.40.0-6) ... Setting up perl-base (5.40.0-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5169 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14.2.0-8_amd64.deb ... Unpacking gcc-14-base:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up gcc-14-base:amd64 (14.2.0-8) ... (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 ... 5169 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-8_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up libstdc++6:amd64 (14.2.0-8) ... (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 ... 5169 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.2.0-8_amd64.deb ... Unpacking libgcc-s1:amd64 (14.2.0-8) over (14.2.0-6) ... Setting up libgcc-s1:amd64 (14.2.0-8) ... (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 ... 5169 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.0.1-3_all.deb ... Unpacking libaudit-common (1:4.0.1-3) over (1:3.1.2-4) ... Setting up libaudit-common (1:4.0.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5169 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-3+b1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-3+b1) over (0.8.5-3) ... Setting up libcap-ng0:amd64 (0.8.5-3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5170 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.1-3_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.1-3) over (1:3.1.2-4+b1) ... Setting up libaudit1:amd64 (1:4.0.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5169 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.273_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.273) over (0.272+b1) ... Setting up libdebconfclient0:amd64 (0.273) ... (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 ... 5168 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1+b3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1+b3) over (2.5.5-1+b2) ... Setting up libseccomp2:amd64 (2.5.5-1+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5168 files and directories currently installed.) Preparing to unpack .../libselinux1_3.7-3+b1_amd64.deb ... Unpacking libselinux1:amd64 (3.7-3+b1) over (3.7-3) ... Setting up libselinux1:amd64 (3.7-3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5169 files and directories currently installed.) Preparing to unpack .../tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) over (2024a-4) ... Preparing to unpack .../libsemanage2_3.7-2+b1_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2+b1) over (3.7-2) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 15 03:21:53 UTC 2024. Universal Time is now: Fri Nov 15 03:21:53 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsemanage2:amd64 (3.7-2+b1) ... Processing triggers for libc-bin (2.40-3) ... 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-yf', 'dist-upgrade'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s DUMP: 5f5a7a5a4b6b5f55629b892089bcb3e7 - 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s INFO: Running scripts post_setup 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s 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 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_dummy_users'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_forbid_home'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.8s 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' 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_minimize'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_minimize'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_zz_backports'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_setup_zz_backports'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-3 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-7 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m6.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m6.3s INFO: Running scripts is_testable 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s INFO: Running scripts pre_test 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_test_root_password'] 0m6.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_test_root_password'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tcgabiolinks'] 0m6.7s DUMP: Package: r-bioc-tcgabiolinks Version: 2.32.0+dfsg-2 Installed-Size: 6550 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-downloader (>= 0.4), r-bioc-biomart, r-cran-dplyr, r-cran-tibble, r-bioc-genomicranges, r-cran-xml (>= 3.98.0), r-cran-data.table, r-cran-jsonlite (>= 1.0.0), r-cran-plyr, r-cran-knitr, r-cran-ggplot2, r-cran-stringr (>= 1.0.0), r-bioc-iranges, r-cran-rvest (>= 0.3.0), r-bioc-s4vectors, r-cran-r.utils, r-bioc-summarizedexperiment (>= 1.4.0), r-bioc-tcgabiolinksgui.data (>= 1.15.1), r-cran-readr, r-cran-tidyr, r-cran-purrr, r-cran-xml2, r-cran-httr (>= 1.2.1) Suggests: r-cran-jpeg, r-cran-png, r-bioc-biocstyle, r-cran-rmarkdown, r-cran-devtools, r-cran-parmigene, r-bioc-biobase, r-bioc-affy, r-cran-testthat, r-bioc-annotationhub, r-bioc-experimenthub, r-cran-seurat, r-bioc-complexheatmap, r-cran-circlize, r-bioc-consensusclusterplus, r-cran-igraph, r-bioc-limma, r-bioc-edger, r-bioc-sva, r-bioc-edaseq, r-cran-survminer, r-bioc-genefilter, r-cran-gridextra, r-cran-survival, r-cran-doparallel, r-cran-ggrepel (>= 0.6.3), r-cran-scales, r-cran-dt Description-en: GNU R/Bioconductor package for integrative analysis with GDC data The aim of TCGAbiolinks is: 1) facilitate the GDC open-access data retrieval, 2) prepare the data using the appropriate pre-processing strategies, 3) provide the means to carry out different standard analyses and 4) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines. Description-md5: a12bea649d7df136b7f6898c8a08d8c7 Homepage: https://bioconductor.org/packages/TCGAbiolinks/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tcgabiolinks/r-bioc-tcgabiolinks_2.32.0+dfsg-2_all.deb Size: 6299404 MD5sum: 3a1990425990ffd849e39807ad7d396a SHA256: 60256b7cf7f92972e6638e4215d9fe148baa6246aac2336222849fd401bdb705 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tcgabiolinks'] 0m6.7s INFO: apt-cache knows about the following packages: r-bioc-tcgabiolinks 0m6.7s INFO: Running scripts pre_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m6.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m6.8s DUMP: r-bioc-tcgabiolinks: Installed: (none) Candidate: 2.32.0+dfsg-2 Version table: 2.32.0+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks'] 0m28.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libatomic1 libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv node-normalize.css openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tcgabiolinksgui.data r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-clipr 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-downloader r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr r-cran-hms r-cran-httr r-cran-httr2 r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-readr r-cran-rlang r-cran-rsqlite r-cran-rvest r-cran-scales r-cran-selectr r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 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: libc-devtools glibc-doc manpages-dev low-memory-monitor krb5-doc krb5-user fonts-mathjax-extras fonts-stix libjs-mathjax-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-bioc-all r-bioc-golubesets r-bioc-limma r-cran-testthat r-cran-rmarkdown r-bioc-rtracklayer r-bioc-rsamtools r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-mockery r-cran-httptest2 r-bioc-pwalign r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-biocparallel r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-genomicalignments r-bioc-gviz r-bioc-variantannotation r-bioc-annotationhub r-bioc-dexseq r-bioc-edger r-cran-markdown r-bioc-sparsematrixstats r-bioc-shortread r-bioc-rhdf5 r-cran-jpeg r-cran-devtools r-cran-parmigene r-bioc-experimenthub r-cran-seurat r-bioc-complexheatmap r-cran-circlize r-bioc-consensusclusterplus r-cran-igraph r-bioc-sva r-bioc-edaseq r-cran-survminer r-cran-gridextra r-cran-survival r-cran-doparallel r-cran-ggrepel r-cran-dt r-cran-rmariadb r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-rstudioapi r-cran-rmysql r-cran-microbenchmark r-cran-lubridate r-cran-magick r-cran-sf r-cran-getopt r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-codetools r-cran-inline r-cran-bench r-cran-brio r-cran-callr r-cran-here r-cran-htmltools r-cran-pkgbuild r-cran-pkgload readline-doc Recommended packages: manpages manpages-dev 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-cran-testthat r-cran-callr r-cran-covr r-cran-htmltools r-cran-htmlwidgets r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown 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-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-xts r-cran-zoo r-cran-markdown r-cran-rmariadb r-cran-rpostgresql r-cran-broom r-cran-rmysql r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-waldo r-cran-testit r-cran-docopt r-cran-promises r-cran-webfakes r-cran-r.rsp r-cran-bslib r-cran-codetools r-cran-formatr r-cran-gridsvg r-cran-magick r-cran-reticulate r-cran-rgl r-cran-sass r-cran-tikzdevice r-cran-tinytex r-cran-webshot node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-microbenchmark r-cran-r.devices r-cran-sodium r-cran-lubridate r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-fs r-cran-usethis r-cran-dbitest r-cran-gert r-cran-gh r-cran-dichromat r-cran-mockr r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-commonmark r-cran-remotes r-cran-renv r-cran-runit 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 fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libatomic1 libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv node-normalize.css openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tcgabiolinks r-bioc-tcgabiolinksgui.data r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-clipr 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-downloader r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr r-cran-hms r-cran-httr r-cran-httr2 r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-readr r-cran-rlang r-cran-rsqlite r-cran-rvest r-cran-scales r-cran-selectr r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 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, 203 newly installed, 0 to remove and 0 not upgraded. Need to get 210 MB of archives. After this operation, 418 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:18 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.11.5-1 [2443 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-3 [1956 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:38 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:75 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get:92 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:127 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:130 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:133 http://deb.debian.org/debian trixie/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-2 [1542 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 r-cran-dbplyr all 2.5.0+dfsg-1 [1247 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [301 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-httr2 all 1.0.5-1 [654 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-bioc-biomart all 2.60.1+dfsg-1 [452 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1842 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-downloader all 0.4-4 [24.6 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.49+dfsg-1 [546 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.48+dfsg-1 [912 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-61-1 [1112 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 r-cran-selectr all 0.4-2-2 [412 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 r-cran-rvest all 1.0.4-1 [304 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 r-cran-r.oo all 1.26.0-1 [961 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 r-cran-r.utils all 2.12.3-1 [1396 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 r-bioc-tcgabiolinksgui.data all 1.24.0+dfsg-1 [22.5 MB] Get:199 http://deb.debian.org/debian trixie/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 r-cran-tzdb amd64 0.4.0-2 [499 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 r-cran-vroom amd64 1.6.5-1 [830 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 r-cran-readr amd64 2.1.5-1 [759 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 r-bioc-tcgabiolinks all 2.32.0+dfsg-2 [6299 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 210 MB in 3s (81.6 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 ... 5162 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package ucf. Preparing to unpack .../004-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 .../005-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../006-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../007-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../014-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../015-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../016-libatomic1_14.2.0-8_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-8) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../017-libblas3_3.12.0-3+b1_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3+b1) ... Selecting previously unselected package libc-dev-bin. Preparing to unpack .../018-libc-dev-bin_2.40-3_amd64.deb ... Unpacking libc-dev-bin (2.40-3) ... Selecting previously unselected package linux-libc-dev. Preparing to unpack .../019-linux-libc-dev_6.11.5-1_all.deb ... Unpacking linux-libc-dev (6.11.5-1) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../020-libcrypt-dev_1%3a4.4.36-5_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.36-5) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../021-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 .../022-libc6-dev_2.40-3_amd64.deb ... Unpacking libc6-dev:amd64 (2.40-3) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../023-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../024-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../025-libxdmcp6_1%3a1.1.2-3+b2_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3+b2) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../026-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../027-libx11-data_2%3a1.8.10-2_all.deb ... Unpacking libx11-data (2:1.8.10-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../028-libx11-6_2%3a1.8.10-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-2) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../029-libxcb-render0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../030-libxcb-shm0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../031-libxext6_2%3a1.3.4-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../032-libxrender1_1%3a0.9.10-1.1+b2_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1+b2) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../033-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../034-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../035-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../036-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../037-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../038-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../039-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../040-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../041-libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../042-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../043-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../044-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../045-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../046-libcurl4t64_8.11.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.11.0-1) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../047-libdatrie1_0.2.13-3+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../048-libdeflate0_1.22-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.22-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../049-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../050-libgfortran5_14.2.0-8_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-8) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../051-libglib2.0-0t64_2.82.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../052-libgomp1_14.2.0-8_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-8) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../053-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../075-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../076-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... Selecting previously unselected package libtcl8.6:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../082-libxft2_2.3.6-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b2) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../083-libxss1_1%3a1.2.3-1+b2_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../084-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../085-libxml2_2.12.7+dfsg+really2.9.14-0.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... 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Setting up r-cran-httr2 (1.0.5-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-dplyr (1.1.4-2) ... Setting up r-cran-rsqlite (2.3.7-2) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-r.utils (2.12.3-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up r-cran-rvest (1.0.4-1) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-cran-dbplyr (2.5.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up r-bioc-biocfilecache (2.12.0+dfsg-1) ... Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-bioc-keggrest (1.44.1+dfsg-1) ... Setting up r-bioc-annotationdbi (1.66.0-1) ... Setting up r-bioc-biomart (2.60.1+dfsg-1) ... Setting up r-bioc-tcgabiolinks (2.32.0+dfsg-2) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks'] 0m28.9s INFO: Running scripts post_install 0m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m29.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m30.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m30.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpsr2gesox to sid 0m30.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m30.2s INFO: Running scripts pre_distupgrade 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'update'] 0m33.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7333 kB] Fetched 17.6 MB in 2s (7707 kB/s) Reading package lists... 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'update'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-yf', 'dist-upgrade'] 0m38.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bsdutils libapt-pkg6.0t64 libaudit-common libaudit1 libblkid1 libglib2.0-0t64 libgnutls30t64 libmount1 libpcre2-8-0 libsmartcols1 libsystemd0 libudev1 libuuid1 libxml2 linux-libc-dev login mount r-base-core r-bioc-genomicranges r-cran-rcpp util-linux 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 43.7 MB of archives. After this operation, 121 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-11 [168 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-11 [199 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB] Get:6 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-11 [1213 kB] Get:7 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-11 [155 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc1-4 [446 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc1-4 [146 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.11 [1043 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:12 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.11 [1362 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB] Get:15 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-11 [81.5 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-2 [275 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:19 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.11.7-1 [2454 kB] Get:20 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:21 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.2+dfsg-1 [1843 kB] Get:22 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.7 MB in 0s (191 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 26497 files and directories currently installed.) Preparing to unpack .../0-libglib2.0-0t64_2.82.2-3_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.2-2) ... Preparing to unpack .../1-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) over (2.12.7+dfsg+really2.9.14-0.1) ... Preparing to unpack .../2-linux-libc-dev_6.11.7-1_all.deb ... Unpacking linux-libc-dev (6.11.7-1) over (6.11.5-1) ... Preparing to unpack .../3-r-base-core_4.4.2-1_amd64.deb ... Unpacking r-base-core (4.4.2-1) over (4.4.1-3) ... Preparing to unpack .../4-r-bioc-genomicranges_1.56.2+dfsg-1_amd64.deb ... Unpacking r-bioc-genomicranges (1.56.2+dfsg-1) over (1.56.1+dfsg-1) ... Preparing to unpack .../5-r-cran-rcpp_1.0.13-1-1_amd64.deb ... Unpacking r-cran-rcpp (1.0.13-1-1) over (1.0.13-1) ... Setting up linux-libc-dev (6.11.7-1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up r-base-core (4.4.2-1) ... Installing new version of config file /etc/R/Makeconf ... Setting up mount (2.40.2-11) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up login (1:4.16.0-2+really2.40.2-11) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-bioc-genomicranges (1.56.2+dfsg-1) ... Processing triggers for libc-bin (2.40-3) ... 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-yf', 'dist-upgrade'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.3s DUMP: 04f19e8eed03ff405e8ee8f9812ff0ca - 0m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tcgabiolinks'] 0m39.6s DUMP: Package: r-bioc-tcgabiolinks Version: 2.32.0+dfsg-2 Installed-Size: 6550 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-downloader (>= 0.4), r-bioc-biomart, r-cran-dplyr, r-cran-tibble, r-bioc-genomicranges, r-cran-xml (>= 3.98.0), r-cran-data.table, r-cran-jsonlite (>= 1.0.0), r-cran-plyr, r-cran-knitr, r-cran-ggplot2, r-cran-stringr (>= 1.0.0), r-bioc-iranges, r-cran-rvest (>= 0.3.0), r-bioc-s4vectors, r-cran-r.utils, r-bioc-summarizedexperiment (>= 1.4.0), r-bioc-tcgabiolinksgui.data (>= 1.15.1), r-cran-readr, r-cran-tidyr, r-cran-purrr, r-cran-xml2, r-cran-httr (>= 1.2.1) Suggests: r-cran-jpeg, r-cran-png, r-bioc-biocstyle, r-cran-rmarkdown, r-cran-devtools, r-cran-parmigene, r-bioc-biobase, r-bioc-affy, r-cran-testthat, r-bioc-annotationhub, r-bioc-experimenthub, r-cran-seurat, r-bioc-complexheatmap, r-cran-circlize, r-bioc-consensusclusterplus, r-cran-igraph, r-bioc-limma, r-bioc-edger, r-bioc-sva, r-bioc-edaseq, r-cran-survminer, r-bioc-genefilter, r-cran-gridextra, r-cran-survival, r-cran-doparallel, r-cran-ggrepel (>= 0.6.3), r-cran-scales, r-cran-dt Description-en: GNU R/Bioconductor package for integrative analysis with GDC data The aim of TCGAbiolinks is: 1) facilitate the GDC open-access data retrieval, 2) prepare the data using the appropriate pre-processing strategies, 3) provide the means to carry out different standard analyses and 4) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines. Description-md5: a12bea649d7df136b7f6898c8a08d8c7 Homepage: https://bioconductor.org/packages/TCGAbiolinks/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tcgabiolinks/r-bioc-tcgabiolinks_2.32.0+dfsg-2_all.deb Size: 6299404 MD5sum: 3a1990425990ffd849e39807ad7d396a SHA256: 60256b7cf7f92972e6638e4215d9fe148baa6246aac2336222849fd401bdb705 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tcgabiolinks'] 0m39.6s INFO: apt-cache knows about the following packages: r-bioc-tcgabiolinks 0m39.6s INFO: Running scripts pre_install 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m39.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m39.7s DUMP: r-bioc-tcgabiolinks: Installed: 2.32.0+dfsg-2 Candidate: 2.32.0+dfsg-2 Version table: *** 2.32.0+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks'] 0m40.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-tcgabiolinks is already the newest version (2.32.0+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks'] 0m40.4s INFO: Running scripts post_install 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m40.4s INFO: Running scripts post_distupgrade 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m40.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_exceptions'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m40.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_distupgrade_zz_backports'] 0m40.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m42.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m42.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m43.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m43.2s INFO: Running scripts pre_install 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_database-server'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_exceptions'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_extras'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m43.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m43.4s DUMP: r-bioc-tcgabiolinks: Installed: 2.32.0+dfsg-2 Candidate: 2.32.0+dfsg-2 Version table: *** 2.32.0+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-cache', 'policy', 'r-bioc-tcgabiolinks'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks=2.32.0+dfsg-2'] 0m43.9s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-tcgabiolinks is already the newest version (2.32.0+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', '-y', 'install', 'r-bioc-tcgabiolinks=2.32.0+dfsg-2'] 0m43.9s INFO: Running scripts post_install 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_install_exceptions'] 0m43.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m45.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m46.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', '-ac', '--ignore-obsolete'] 0m49.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', '-ac', '--ignore-obsolete'] 0m49.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m49.1s DUMP: 0.15.6 0m49.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m49.1s INFO: Running adequate version 0.15.6 now. 0m49.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'r-bioc-tcgabiolinks'] 0m49.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'r-bioc-tcgabiolinks'] 0m49.2s INFO: Running scripts pre_remove 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m52.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m52.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m52.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m52.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_exceptions'] 0m52.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/pre_remove_exceptions'] 0m52.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m52.4s DUMP: install ok installed apt apt 2.9.11 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1+b1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.11 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblas3:amd64 libblas3 3.12.0-3+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc-dev-bin libc-dev-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libc6-dev:amd64 libc6-dev 2.40-3 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl4t64:amd64 libcurl4t64 8.11.0-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-3 install ok installed libpaper-utils libpaper-utils 1.1.29+b2 install ok installed libpaper1:amd64 libpaper1 1.1.29+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc1-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libudev1:amd64 libudev1 257~rc1-4 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed linux-libc-dev linux-libc-dev 6.11.7-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-7 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.66.0-1 install ok installed r-bioc-biobase r-bioc-biobase 2.64.0-4 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.12.0+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-2 install ok installed r-bioc-biomart r-bioc-biomart 2.60.1+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.72.1+dfsg-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.30.1+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.40.1+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.12-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.56.2+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.38.1-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.44.1+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.16.0-2 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.4.1+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.42.1+dfsg-2 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.4.8+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.34.0+dfsg-1 install ok installed r-bioc-tcgabiolinks r-bioc-tcgabiolinks 2.32.0+dfsg-2 install ok installed r-bioc-tcgabiolinksgui.data r-bioc-tcgabiolinksgui.data 1.24.0+dfsg-1 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.0.0+ds-2 install ok installed r-bioc-xvector r-bioc-xvector 0.44.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.50.0+dfsg-2 install ok installed r-cran-abind r-cran-abind 1.4-8-1 install ok installed r-cran-askpass r-cran-askpass 1.2.1-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-cachem r-cran-cachem 1.1.0-1 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-clipr r-cran-clipr 0.8.0-1 install ok installed r-cran-colorspace r-cran-colorspace 2.1-1+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.5.0-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.2.3+dfsg-1 install ok installed r-cran-data.table r-cran-data.table 1.16.2+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.2.3-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.5.0+dfsg-1 install ok installed r-cran-digest r-cran-digest 0.6.37-1 install ok installed r-cran-downloader r-cran-downloader 0.4-4 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-2 install ok installed r-cran-evaluate r-cran-evaluate 1.0.0-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-farver r-cran-farver 2.1.2-1 install ok installed r-cran-fastmap r-cran-fastmap 1.2.0-1 install ok installed r-cran-filelock r-cran-filelock 1.0.3-1 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.5.1+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-gtable r-cran-gtable 0.3.6+dfsg-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-httr2 r-cran-httr2 1.0.5-1 install ok installed r-cran-isoband r-cran-isoband 0.2.7-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.9+dfsg-1 install ok installed r-cran-knitr r-cran-knitr 1.48+dfsg-1 install ok installed r-cran-labeling r-cran-labeling 0.4.3-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-mass r-cran-mass 7.3-61-1 install ok installed r-cran-matrix r-cran-matrix 1.7-1-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.4.1-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-mime r-cran-mime 0.12-2 install ok installed r-cran-munsell r-cran-munsell 0.5.1-1 install ok installed r-cran-nlme r-cran-nlme 3.1.166-1 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.4-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-plyr r-cran-plyr 1.8.9-1 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-r.methodss3 r-cran-r.methodss3 1.8.2-1 install ok installed r-cran-r.oo r-cran-r.oo 1.26.0-1 install ok installed r-cran-r.utils r-cran-r.utils 2.12.3-1 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 1.0.13-1-1 install ok installed r-cran-readr r-cran-readr 2.1.5-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.7-2 install ok installed r-cran-rvest r-cran-rvest 1.0.4-1 install ok installed r-cran-scales r-cran-scales 1.3.0-1 install ok installed r-cran-selectr r-cran-selectr 0.4-2-2 install ok installed r-cran-stringi r-cran-stringi 1.8.4-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-sys r-cran-sys 3.4.3-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-tzdb r-cran-tzdb 0.4.0-2 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-viridislite r-cran-viridislite 0.4.2-2 install ok installed r-cran-vroom r-cran-vroom 1.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.2+dfsg-1 install ok installed r-cran-xfun r-cran-xfun 0.49+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.17-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.6-1 install ok installed r-cran-yaml r-cran-yaml 2.3.10-1 install ok installed readline-common readline-common 8.2-5 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 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 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1 0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-mathjax', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-mathjax', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'node-normalize.css', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tcgabiolinksgui.data', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-clipr', '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-downloader', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-highr', 'r-cran-hms', 'r-cran-httr', 'r-cran-httr2', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-readr', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-rvest', 'r-cran-scales', 'r-cran-selectr', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-xfun', '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-tcgabiolinks'] 0m54.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libatomic1 libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv node-normalize.css openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-tcgabiolinks r-bioc-tcgabiolinksgui.data r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-clipr 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-downloader r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr r-cran-hms r-cran-httr r-cran-httr2 r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-readr r-cran-rlang r-cran-rsqlite r-cran-rvest r-cran-scales r-cran-selectr r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-vroom r-cran-withr r-cran-xfun 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, 203 to remove and 0 not upgraded. After this operation, 418 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 ... 26498 files and directories currently installed.) Removing r-bioc-tcgabiolinks (2.32.0+dfsg-2) ... Removing r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Removing r-bioc-delayedarray (0.30.1+dfsg-1) ... Removing r-bioc-sparsearray (1.4.8+dfsg-1) ... Removing r-bioc-s4arrays (1.4.1+dfsg-1) ... Removing r-cran-abind (1.4-8-1) ... Removing r-cran-ggplot2 (3.5.1+dfsg-1) ... Removing r-cran-scales (1.3.0-1) ... Removing r-cran-rcolorbrewer (1.1-3-1) ... Removing r-cran-readr (2.1.5-1) ... Removing r-cran-knitr (1.48+dfsg-1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-bioc-biomart (2.60.1+dfsg-1) ... Removing r-cran-httr2 (1.0.5-1) ... Removing r-bioc-genomicranges (1.56.2+dfsg-1) ... Removing r-bioc-annotationdbi (1.66.0-1) ... Removing r-bioc-keggrest (1.44.1+dfsg-1) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing r-bioc-xvector (0.44.0-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libc6-dev:amd64 (2.40-3) ... Removing libc-dev-bin (2.40-3) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing r-cran-data.table (1.16.2+dfsg-1) ... Removing r-bioc-biocfilecache (2.12.0+dfsg-1) ... Removing r-cran-dbplyr (2.5.0+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-cran-rvest (1.0.4-1) ... Removing r-cran-selectr (0.4-2-2) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.4-1) ... Removing r-cran-xml2 (1.3.6-1) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-highlight.js (9.18.5+dfsg1-2) ... Removing libjs-jquery-datatables (1.11.5+dfsg-2) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing r-cran-png (0.1-8-1+b1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing linux-libc-dev (6.11.7-1) ... Removing littler (0.3.20-1) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing r-bioc-biobase (2.64.0-4) ... Removing r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Removing r-bioc-ucsc.utils (1.0.0+ds-2) ... Removing r-bioc-iranges (2.38.1-1) ... Removing r-bioc-s4vectors (0.42.1+dfsg-2) ... Removing r-bioc-tcgabiolinksgui.data (1.24.0+dfsg-1) ... Removing r-bioc-matrixgenerics (1.16.0-2) ... Removing r-bioc-biocgenerics (0.50.0-2) ... Removing r-bioc-genomeinfodbdata (1.2.12-1) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... Removing r-cran-askpass (1.2.1-1) ... Removing r-cran-vroom (1.6.5-1) ... Removing r-cran-rsqlite (2.3.7-2) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.1.0-1) ... Removing r-cran-dplyr (1.1.4-2) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-clipr (0.8.0-1) ... Removing r-cran-munsell (0.5.1-1) ... Removing r-cran-colorspace (2.1-1+dfsg-1) ... Removing r-cran-tzdb (0.4.0-2) ... Removing r-cran-cpp11 (0.5.0-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-dbi (1.2.3-1) ... Removing r-cran-downloader (0.4-4) ... Removing r-cran-digest (0.6.37-1) ... Removing r-cran-evaluate (1.0.0-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-farver (2.1.2-1) ... Removing r-cran-fastmap (1.2.0-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-gtable (0.3.6+dfsg-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-isoband (0.2.7-1) ... Removing r-cran-jsonlite (1.8.9+dfsg-1) ... Removing r-cran-labeling (0.4.3-1) ... Removing r-cran-nlme (3.1.166-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mass (7.3-61-1) ... Removing r-cran-matrixstats (1.4.1-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-plyr (1.8.9-1) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-r.utils (2.12.3-1) ... Removing r-cran-r.oo (1.26.0-1) ... Removing r-cran-r.methodss3 (1.8.2-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sys (3.4.3-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-viridislite (0.4.2-2) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing r-cran-xfun (0.49+dfsg-1) ... Removing r-cran-yaml (2.3.10-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-cran-rcpp (1.0.13-1-1) ... Removing r-cran-curl (5.2.3+dfsg-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-cli (3.6.3-1) ... Removing r-base-core (4.4.2-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-3) ... Removing fontconfig (2.15.0-1.1+b1) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing liblapack3:amd64 (3.12.0-3+b1) ... Removing libblas3:amd64 (3.12.0-3+b1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.11.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpaper-utils (1.1.29+b2) ... Removing libpaper1:amd64 (1.1.29+b2) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing openssl (3.3.2-2) ... Removing readline-common (8.2-5) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b2) ... Processing triggers for libc-bin (2.40-3) ... 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-mathjax', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-mathjax', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'node-normalize.css', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tcgabiolinksgui.data', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-clipr', '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-downloader', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-highr', 'r-cran-hms', 'r-cran-httr', 'r-cran-httr2', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-readr', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-rvest', 'r-cran-scales', 'r-cran-selectr', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-xfun', '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-tcgabiolinks'] 0m54.4s INFO: Running scripts post_remove 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_remove_exceptions'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_remove_exceptions'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-mathjax', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-mathjax', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'node-normalize.css', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tcgabiolinksgui.data', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-clipr', '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-downloader', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-highr', 'r-cran-hms', 'r-cran-httr', 'r-cran-httr2', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-readr', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-rvest', 'r-cran-scales', 'r-cran-selectr', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-xfun', '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'] 0m55.0s DUMP: (Reading database ... 5202 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.15.0-1.1+b1) ... Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-glyphicons-halflings which isn't installed dpkg: warning: ignoring request to remove fonts-mathjax 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 libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-3) ... 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 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b 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 libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed dpkg: warning: ignoring request to remove libjs-highlight.js which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-datatables which isn't installed dpkg: warning: ignoring request to remove libjs-mathjax which isn't installed 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 libnghttp2-14 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+b2) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove 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 (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove node-normalize.css which isn't installed Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for r-base-core (4.4.2-1) ... dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocfilecache which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-tcgabiolinksgui.data which isn't installed dpkg: warning: ignoring request to remove r-bioc-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-clipr 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-downloader 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-evaluate which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-filelock which isn't installed dpkg: warning: ignoring request to remove r-cran-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-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-highr which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-httr2 which isn't installed dpkg: warning: ignoring request to remove r-cran-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-knitr which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-plyr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-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-r.methodss3 which isn't installed dpkg: warning: ignoring request to remove r-cran-r.oo which isn't installed dpkg: warning: ignoring request to remove r-cran-r.utils 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-readr 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-rvest 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-selectr which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-tzdb which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-vroom which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xfun which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-5) ... 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+23.1) ... 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 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-glyphicons-halflings', 'fonts-mathjax', 'libatomic1:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-mathjax', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'node-normalize.css', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-tcgabiolinksgui.data', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-clipr', '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-downloader', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-highr', 'r-cran-hms', 'r-cran-httr', 'r-cran-httr2', 'r-cran-isoband', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-plyr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r.methodss3', 'r-cran-r.oo', 'r-cran-r.utils', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-readr', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-rvest', 'r-cran-scales', 'r-cran-selectr', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tzdb', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-vroom', 'r-cran-withr', 'r-cran-xfun', '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'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', 'r-bioc-tcgabiolinks'] 0m55.0s DUMP: dpkg: warning: ignoring request to remove r-bioc-tcgabiolinks which isn't installed 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', 'r-bioc-tcgabiolinks'] 0m55.0s INFO: Running scripts post_purge 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_purge_exceptions'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_purge_exceptions'] 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', '--pending'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--purge', '--pending'] 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--remove', '--pending'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg', '--remove', '--pending'] 0m55.1s INFO: Running scripts post_test 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_test_exceptions'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'tmp/scripts/post_test_exceptions'] 0m55.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m55.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-divert', '--list'] 0m55.4s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'dpkg-divert', '--list'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'clean'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsr2gesox', 'apt-get', 'clean'] 0m55.5s DEBUG: Recording chroot state 0m56.0s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 0m56.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/shm'] 0m56.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/shm'] 0m56.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/console'] 0m56.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/console'] 0m56.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/ptmx'] 0m56.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/ptmx'] 0m56.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/pts'] 0m56.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/dev/pts'] 0m56.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/proc'] 0m56.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsr2gesox/proc'] 0m56.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m56.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpsr2gesox'] 0m56.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpsr2gesox 0m56.6s INFO: PASS: Upgrading between Debian distributions. 0m56.6s INFO: PASS: All tests. 0m56.6s INFO: piuparts run ends. ret=0 End: 2024-11-15 03:22:45 GMT