Start: 2024-12-07 15:13:04 GMT [testing] Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description: Subclonal copy number and LOH prediction from whole genome sequencing Homepage: https://bioconductor.org/packages/TitanCNA/ Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b [sid] Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description: Subclonal copy number and LOH prediction from whole genome sequencing Homepage: https://bioconductor.org/packages/TitanCNA/ Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/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-titancna=1.42.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-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-titancna=1.42.0-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmpp4vvfw8s 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpp4vvfw8s 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpp4vvfw8s/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9338 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6268 kB] Fetched 15.8 MB in 1s (18.9 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libdebconfclient0 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 10.1 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.274 [10.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.1 kB in 0s (691 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5142 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.274_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.274) over (0.273) ... Setting up libdebconfclient0:amd64 (0.274) ... Processing triggers for libc-bin (2.40-4) ... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 27259aa3632fd0eef569aee38fa36ee0 - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s 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 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 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 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 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 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 2.9.16 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 libblkid1:amd64 libblkid1 2.40.2-11 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 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 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 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 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-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 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 2.40.2-11 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 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 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 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 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~rc3-1 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 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 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+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.2~rc1-2 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 openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 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-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/is_testable_uninstallable'] 0m3.3s INFO: Running scripts pre_test 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m3.5s DUMP: Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description-en: Subclonal copy number and LOH prediction from whole genome sequencing Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Homepage: https://bioconductor.org/packages/TitanCNA/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m3.5s INFO: apt-cache knows about the following packages: r-bioc-titancna 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 0m3.5s 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: 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m3.6s DUMP: r-bioc-titancna: Installed: (none) Candidate: 1.42.0-1 Version table: 1.42.0-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m50.2s 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-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libasan8 libatomic1 libbibtex-parser-perl libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libio-string-perl libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblsan0 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.40 r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome r-cran-foreach r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-promises r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: apache2 | lighttpd | httpd libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libc-devtools glibc-doc manpages-dev gdbm-l10n low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc libmpfi-doc libstdc++-14-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex citation-style-language-styles perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl 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-all r-bioc-golubesets r-bioc-limma r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-testthat r-cran-bbmisc r-cran-doparallel r-bioc-shortread r-cran-batchtools r-bioc-pwalign r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-cran-r.utils r-bioc-edger r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-rhdf5 r-cran-rmariadb r-bioc-snpstats r-cran-ggplot2 r-cran-magick r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-rstudioapi r-cran-rmysql r-cran-microbenchmark r-cran-getopt r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-scales r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-bench r-cran-brio r-cran-callr r-cran-here r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-plm r-cran-zoo readline-doc debhelper ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc wp2latex Recommended packages: manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs node-jquery krb5-locales libldap-common publicsuffix libsasl2-modules netbase r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-remotes r-cran-downlit r-cran-htmlwidgets r-cran-rstudioapi r-cran-miniui r-cran-rsconnect r-cran-testit r-cran-tufte r-cran-xml2 r-cran-webshot r-cran-future r-cran-ggplot2 r-cran-thematic r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps r-cran-rprojroot r-cran-whoami r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-scales r-cran-spelling r-cran-webutils r-cran-r.utils r-cran-xts r-cran-zoo r-cran-markdown r-cran-broom r-cran-dbplyr r-cran-purrr r-cran-rmysql r-cran-rpostgresql r-cran-stringi r-cran-tidyr r-cran-unitizer r-cran-rsvg r-cran-survival r-cran-pkgload r-cran-waldo r-cran-cairo r-cran-ragg r-cran-jpeg r-cran-readr r-cran-r.rsp r-cran-sf r-cran-gridsvg r-cran-magick r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-svglite node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-microbenchmark r-cran-r.devices r-cran-sodium r-cran-lubridate r-cran-runit r-cran-usethis r-cran-dygraphs r-cran-dbitest r-cran-gert r-cran-gh r-cran-hms r-cran-rvest r-cran-dt r-cran-mockr r-cran-formattable r-cran-stringr r-cran-pkgdown r-cran-zeallot r-cran-renv lmodern dvisvgm 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-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libasan8 libatomic1 libbibtex-parser-perl libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libio-string-perl libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblsan0 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.40 r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-titancna r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome r-cran-foreach r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-promises r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 268 newly installed, 0 to remove and 0 not upgraded. Need to get 379 MB of archives. After this operation, 1206 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 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:25 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:27 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 liblatex-tounicode-perl all 0.55-1 [28.8 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libbibtex-parser-perl all 1.05+dfsg-1 [17.4 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-4 [52.0 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.11.10-1 [2461 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-4 [1954 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b2 [10.6 MB] Get:46 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:47 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:61 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:93 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libjs-lunr all 2.3.9~dfsg-2 [76.6 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.7-1+b1 [147 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:115 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:182 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:185 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:188 http://deb.debian.org/debian trixie/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:198 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.49+dfsg-1 [546 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.49+dfsg-1 [861 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 r-cran-tinytex all 0.53-1 [146 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 r-cran-shiny all 1.9.1+dfsg-1 [3126 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1474 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 r-cran-bookdown all 0.41+dfsg-1 [1404 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get:232 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 texlive-bibtex-extra all 2024.20241115-1 [80.0 MB] Get:234 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocversion all 3.19.1-1 [10.9 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [453 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1842 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 r-cran-bitops amd64 1.0-8-1 [30.7 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 r-bioc-bsgenome all 1.72.0-1 [6812 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [918 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 r-bioc-variantannotation amd64 1.50.0-1 [3508 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-2 [1542 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 r-bioc-titancna amd64 1.42.0-1 [3911 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 379 MB in 12s (31.1 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 ... 5146 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 perl-modules-5.40. Preparing to unpack .../004-perl-modules-5.40_5.40.0-8_all.deb ... Unpacking perl-modules-5.40 (5.40.0-8) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../005-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../006-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../007-libperl5.40_5.40.0-8_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-8) ... Selecting previously unselected package perl. Preparing to unpack .../008-perl_5.40.0-8_amd64.deb ... Unpacking perl (5.40.0-8) ... Selecting previously unselected package ucf. Preparing to unpack .../009-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 .../010-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../011-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 .../012-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 .../013-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 .../014-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 .../015-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../016-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 .../017-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 .../018-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../019-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../020-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-lmodern. Preparing to unpack .../021-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../022-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package javascript-common. Preparing to unpack .../023-javascript-common_11+nmu1_all.deb ... Unpacking javascript-common (11+nmu1) ... Selecting previously unselected package libasan8:amd64. Preparing to unpack .../024-libasan8_14.2.0-8_amd64.deb ... Unpacking libasan8:amd64 (14.2.0-8) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../025-libatomic1_14.2.0-8_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-8) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../026-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package liblatex-tounicode-perl. Preparing to unpack .../027-liblatex-tounicode-perl_0.55-1_all.deb ... Unpacking liblatex-tounicode-perl (0.55-1) ... Selecting previously unselected package libbibtex-parser-perl. Preparing to unpack .../028-libbibtex-parser-perl_1.05+dfsg-1_all.deb ... Unpacking libbibtex-parser-perl (1.05+dfsg-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../029-libblas3_3.12.0-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-4) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../030-libgomp1_14.2.0-8_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-8) ... Selecting previously unselected package libitm1:amd64. Preparing to unpack .../031-libitm1_14.2.0-8_amd64.deb ... Unpacking libitm1:amd64 (14.2.0-8) ... Selecting previously unselected package liblsan0:amd64. Preparing to unpack .../032-liblsan0_14.2.0-8_amd64.deb ... Unpacking liblsan0:amd64 (14.2.0-8) ... Selecting previously unselected package libtsan2:amd64. Preparing to unpack .../033-libtsan2_14.2.0-8_amd64.deb ... Unpacking libtsan2:amd64 (14.2.0-8) ... Selecting previously unselected package libubsan1:amd64. Preparing to unpack .../034-libubsan1_14.2.0-8_amd64.deb ... Unpacking libubsan1:amd64 (14.2.0-8) ... Selecting previously unselected package libhwasan0:amd64. Preparing to unpack .../035-libhwasan0_14.2.0-8_amd64.deb ... Unpacking libhwasan0:amd64 (14.2.0-8) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../036-libquadmath0_14.2.0-8_amd64.deb ... Unpacking libquadmath0:amd64 (14.2.0-8) ... Selecting previously unselected package libgcc-14-dev:amd64. 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Preparing to unpack .../116-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../117-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 .../118-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... 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Preparing to unpack .../124-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../125-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../126-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... 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 .../127-libxft2_2.3.6-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b2) ... Selecting previously unselected package libxss1:amd64. 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Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up texlive-bibtex-extra (2024.20241115-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-promises (1.3.0+dfsg-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-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+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-cran-shiny (1.9.1+dfsg-1) ... Setting up r-cran-rmarkdown (2.28+dfsg-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up r-cran-bookdown (0.41+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-biocstyle (2.32.1+dfsg-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Setting up r-bioc-bsgenome (1.72.0-1) ... Setting up r-bioc-variantannotation (1.50.0-1) ... Setting up r-bioc-titancna (1.42.0-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 0m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m50.2s INFO: Running scripts post_install 0m50.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 0m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 0m50.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m52.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m52.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpp4vvfw8s to sid 0m52.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m52.0s INFO: Running scripts pre_distupgrade 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_exceptions'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m52.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'update'] 0m53.9s 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 [7345 kB] Fetched 17.6 MB in 1s (12.6 MB/s) Reading package lists... 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'update'] 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-yf', 'dist-upgrade'] 0m57.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libncursesw6 libproc2-0 procps The following packages have been kept back: r-bioc-biocstyle The following packages will be upgraded: bash bsdutils libblkid1 libgpg-error0 libharfbuzz0b libmount1 libsmartcols1 libunistring5 libuuid1 libzzip-0-13t64 linux-libc-dev login login.defs mount passwd r-bioc-genomicranges r-cran-commonmark ucf util-linux 19 upgraded, 3 newly installed, 0 to remove and 1 not upgraded. Need to get 11.7 MB of archives. After this operation, 3384 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-1 [1501 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-12 [106 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-12 [36.0 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-12 [168 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-12 [199 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-12 [139 kB] Get:7 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-12 [1209 kB] Get:8 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-12 [155 kB] Get:9 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-12 [81.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.51-2 [82.1 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:12 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-7 [185 kB] Get:13 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-7 [1233 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:16 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:17 http://deb.debian.org/debian sid/main amd64 ucf all 3.0045 [45.2 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:20 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.3-1 [2459 kB] 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-commonmark amd64 1.9.2-1 [122 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.7 MB in 1s (9814 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58395 files and directories currently installed.) Preparing to unpack .../bash_5.2.37-1_amd64.deb ... Unpacking bash (5.2.37-1) over (5.2.32-1+b2) ... Setting up bash (5.2.37-1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-12_amd64.deb ... Unpacking bsdutils (1:2.40.2-12) over (1:2.40.2-11) ... Setting up bsdutils (1:2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-12_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libuuid1:amd64 (2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-12_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libblkid1:amd64 (2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-12_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libmount1:amd64 (2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-12_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-12) over (2.40.2-11) ... Setting up libsmartcols1:amd64 (2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58394 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-12_amd64.deb ... Unpacking util-linux (2.40.2-12) over (2.40.2-11) ... Setting up util-linux (2.40.2-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58391 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-12_amd64.deb ... Unpacking mount (2.40.2-12) over (2.40.2-11) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-12_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-12) over (1:4.16.0-2+really2.40.2-11) ... Preparing to unpack .../libgpg-error0_1.51-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.51-2) over (1.50-4) ... Setting up libgpg-error0:amd64 (1.51-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58391 files and directories currently installed.) Preparing to unpack .../libunistring5_1.3-1_amd64.deb ... Unpacking libunistring5:amd64 (1.3-1) over (1.2-1+b1) ... Setting up libunistring5:amd64 (1.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58390 files and directories currently installed.) Preparing to unpack .../00-login.defs_1%3a4.16.0-7_all.deb ... Unpacking login.defs (1:4.16.0-7) over (1:4.16.0-5) ... Preparing to unpack .../01-passwd_1%3a4.16.0-7_amd64.deb ... Unpacking passwd (1:4.16.0-7) over (1:4.16.0-5) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../02-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../03-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../04-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Preparing to unpack .../05-ucf_3.0045_all.deb ... Unpacking ucf (3.0045) over (3.0043+nmu1) ... Preparing to unpack .../06-libharfbuzz0b_10.1.0-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.1.0-1) over (10.0.1-1) ... Preparing to unpack .../07-libzzip-0-13t64_0.13.72+dfsg.1-1.3_amd64.deb ... Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) over (0.13.72+dfsg.1-1.2+b1) ... Preparing to unpack .../08-linux-libc-dev_6.12.3-1_all.deb ... Unpacking linux-libc-dev (6.12.3-1) over (6.11.10-1) ... Preparing to unpack .../09-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 .../10-r-cran-commonmark_1.9.2-1_amd64.deb ... Unpacking r-cran-commonmark (1.9.2-1) over (1.9.1-1) ... Setting up r-bioc-genomicranges (1.56.2+dfsg-1) ... Setting up login.defs (1:4.16.0-7) ... Setting up linux-libc-dev (6.12.3-1) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up passwd (1:4.16.0-7) ... Setting up mount (2.40.2-12) ... Setting up procps (2:4.0.4-6) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up r-cran-commonmark (1.9.2-1) ... Setting up login (1:4.16.0-2+really2.40.2-12) ... Setting up ucf (3.0045) ... Installing new version of config file /etc/ucf.conf ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for debianutils (5.21) ... 0m57.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-yf', 'dist-upgrade'] 0m57.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m57.1s DUMP: ab26f25f331df42cd7291ea40c40155e - 0m57.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m57.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m57.2s DUMP: Package: r-bioc-titancna Version: 1.42.0-1 Installed-Size: 7622 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-variantannotation (>= 1.50.0), r-cran-foreach (>= 1.4.3), r-bioc-genomeinfodb (>= 1.40.1), r-cran-data.table (>= 1.10.4), r-cran-dplyr (>= 0.5.0), libc6 (>= 2.14) Description-en: Subclonal copy number and LOH prediction from whole genome sequencing Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. Description-md5: 1f4507bd0fdc9ecda6e72377aef4d0df Homepage: https://bioconductor.org/packages/TitanCNA/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-titancna/r-bioc-titancna_1.42.0-1_amd64.deb Size: 3911000 MD5sum: 2d1f78b5322d730a16c237022c8c9ae4 SHA256: 155aeaa49b12b6d72e524c83fd53efb60569c3dcbdecb1b8d030cf916f08125b 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-titancna'] 0m57.2s INFO: apt-cache knows about the following packages: r-bioc-titancna 0m57.2s INFO: Running scripts pre_install 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 0m57.3s 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: 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m57.4s DUMP: r-bioc-titancna: Installed: 1.42.0-1 Candidate: 1.42.0-1 Version table: *** 1.42.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m57.6s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-titancna is already the newest version (1.42.0-1). 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna'] 0m57.6s INFO: Running scripts post_install 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 0m57.6s INFO: Running scripts post_distupgrade 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_exceptions'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_exceptions'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_zz_backports'] 0m57.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_distupgrade_zz_backports'] 0m57.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m59.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 0m59.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m1.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m1.0s INFO: Running scripts pre_install 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_database-server'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_exceptions'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_extras'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 1m1.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 1m1.0s DUMP: r-bioc-titancna: Installed: 1.42.0-1 Candidate: 1.42.0-1 Version table: *** 1.42.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-cache', 'policy', 'r-bioc-titancna'] 1m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna=1.42.0-1'] 1m1.3s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-titancna is already the newest version (1.42.0-1). 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', '-y', 'install', 'r-bioc-titancna=1.42.0-1'] 1m1.3s INFO: Running scripts post_install 1m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_install_exceptions'] 1m1.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m5.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', '-ac', '--ignore-obsolete'] 1m8.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', '-ac', '--ignore-obsolete'] 1m8.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m8.8s DUMP: 0.15.6 1m8.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m8.8s INFO: Running adequate version 0.15.6 now. 1m8.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'r-bioc-titancna'] 1m8.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'r-bioc-titancna'] 1m8.8s INFO: Running scripts pre_remove 1m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_exceptions'] 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/pre_remove_exceptions'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m14.3s DUMP: install ok installed apt apt 2.9.16 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 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 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 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-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-lmodern fonts-lmodern 2.005-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-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 javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.16 install ok installed libasan8:amd64 libasan8 14.2.0-8 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 libbibtex-parser-perl libbibtex-parser-perl 1.05+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-3.2+b2 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 2.40-4 install ok installed libc-dev-bin libc-dev-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libc6-dev:amd64 libc6-dev 2.40-4 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 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 0.274 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 1.47.2~rc1-2 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-14-dev:amd64 libgcc-14-dev 14.2.0-8 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 libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 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-3 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 1.51-2 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 10.1.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-8 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 libio-string-perl libio-string-perl 1.08-4 install ok installed libitm1:amd64 libitm1 14.2.0-8 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-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-4 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-es5-shim libjs-es5-shim 4.6.7-2 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-jquery-selectize.js libjs-jquery-selectize.js 0.12.6+dfsg-1.1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-json libjs-json 0~20221030+~1.0.8-1 install ok installed libjs-lunr libjs-lunr 2.3.9~dfsg-2 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libjs-microplugin.js libjs-microplugin.js 0.0.3+dfsg-1.1 install ok installed libjs-modernizr libjs-modernizr 3.13.0-0.1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-6 install ok installed libjs-prettify libjs-prettify 2015.12.04+dfsg-1.1 install ok installed libjs-sifter.js libjs-sifter.js 0.6.0+dfsg-3 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkpathsea6:amd64 libkpathsea6 2024.20240313.70630+ds-5 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 3.12.0-4 install ok installed liblatex-tounicode-perl liblatex-tounicode-perl 0.55-1 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 liblsan0:amd64 liblsan0 14.2.0-8 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.7-1+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 2.40.2-12 install ok installed libmpfi0:amd64 libmpfi0 1.5.4+ds-4 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b2 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 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 libnuma1:amd64 libnuma1 2.0.18-1+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 libpango-1.0-0:amd64 libpango-1.0-0 1.55.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.55.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.55.0+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 10.44-4 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 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 libpotrace0:amd64 libpotrace0 1.16-2+b2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libptexenc1:amd64 libptexenc1 2024.20240313.70630+ds-5 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-8 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 2.5.5-2 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 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 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++-14-dev:amd64 libstdc++-14-dev 14.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsynctex2:amd64 libsynctex2 2024.20240313.70630+ds-5 install ok installed libsystemd0:amd64 libsystemd0 257~rc3-1 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 libteckit0:amd64 libteckit0 2.5.12+ds1-1+b1 install ok installed libtexlua53-5:amd64 libtexlua53-5 2024.20240313.70630+ds-5 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 libtsan2:amd64 libtsan2 14.2.0-8 install ok installed libubsan1:amd64 libubsan1 14.2.0-8 install ok installed libudev1:amd64 libudev1 257~rc3-1 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-7 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 libxaw7:amd64 libxaw7 2:1.0.16-1 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 1:1.1.5-1 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 libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxmu6:amd64 libxmu6 2:1.1.3-3+b3 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1+b2 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 libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed libzzip-0-13t64:amd64 libzzip-0-13t64 0.13.72+dfsg.1-1.3 install ok installed linux-libc-dev linux-libc-dev 6.12.3-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 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-bootstrap-sass node-bootstrap-sass 3.4.3-2 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed pandoc pandoc 3.1.11.1+ds-2 install ok installed pandoc-data pandoc-data 3.1.11.1-3 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed procps procps 2:4.0.4-6 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-biocgenerics r-bioc-biocgenerics 0.50.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.14.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.38.0-2 install ok installed r-bioc-biocstyle r-bioc-biocstyle 2.32.1+dfsg-1 install ok installed r-bioc-biocversion r-bioc-biocversion 3.19.1-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.72.1+dfsg-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.72.0-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.30.1+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.40.1+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.12-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.40.0-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.56.0+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.56.2+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-rhtslib r-bioc-rhtslib 3.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.20.0+dfsg-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.64.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.4.1+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.42.1+dfsg-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-titancna r-bioc-titancna 1.42.0-1 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.0.0+ds-2 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.50.0-1 install ok installed r-bioc-xvector r-bioc-xvector 0.44.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.50.0+dfsg-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-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-biocmanager r-cran-biocmanager 1.30.25+dfsg-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-8-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-bookdown r-cran-bookdown 0.41+dfsg-1 install ok installed r-cran-bslib r-cran-bslib 0.7.0+dfsg-1 install ok installed r-cran-cachem r-cran-cachem 1.1.0-1 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-commonmark r-cran-commonmark 1.9.2-1 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-digest r-cran-digest 0.6.37-1 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-fastmap r-cran-fastmap 1.2.0-1 install ok installed r-cran-fontawesome r-cran-fontawesome 0.5.2-1 install ok installed r-cran-foreach r-cran-foreach 1.5.2-1 install ok installed r-cran-formatr r-cran-formatr 1.14-2 install ok installed r-cran-fs r-cran-fs 1.6.4+dfsg-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.8.0-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-htmltools r-cran-htmltools 0.5.8.1-1 install ok installed r-cran-httpuv r-cran-httpuv 1.6.15+dfsg-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-iterators r-cran-iterators 1.0.14-1 install ok installed r-cran-jquerylib r-cran-jquerylib 0.1.4+dfsg-4 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.9+dfsg-1 install ok installed r-cran-knitr r-cran-knitr 1.49+dfsg-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-later r-cran-later 1.3.2+dfsg-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-matrix r-cran-matrix 1.7-1-1 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-mime r-cran-mime 0.12-2 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.4-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-promises r-cran-promises 1.3.0+dfsg-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.13-1-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.16+dfsg-1 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rjson r-cran-rjson 0.2.23-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.28+dfsg-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.7-2 install ok installed r-cran-sass r-cran-sass 0.4.9+dfsg-1 install ok installed r-cran-shiny r-cran-shiny 1.9.1+dfsg-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-sourcetools r-cran-sourcetools 0.1.7-1-1 install ok installed r-cran-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-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-tinytex r-cran-tinytex 0.53-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.2+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-xtable r-cran-xtable 1:1.8-4-2 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 t1utils t1utils 1.41-4 install ok installed tar tar 1.35+dfsg-3 install ok installed tex-common tex-common 6.18 install ok installed texlive-base texlive-base 2024.20241115-1 install ok installed texlive-bibtex-extra texlive-bibtex-extra 2024.20241115-1 install ok installed texlive-binaries texlive-binaries 2024.20240313.70630+ds-5 install ok installed texlive-latex-base texlive-latex-base 2024.20241115-1 install ok installed tzdata tzdata 2024b-4 install ok installed ucf ucf 3.0045 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 2.40.2-12 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.2.1-2 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 1m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnuma1:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-promises', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-titancna'] 1m16.7s 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-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libasan8 libatomic1 libbibtex-parser-perl libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libio-string-perl libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblsan0 liblua5.4-0 libmpfi0 libmpfr6 libncursesw6 libnghttp2-14 libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpotrace0 libproc2-0 libpsl5t64 libptexenc1 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.40 procps r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-titancna r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome r-cran-foreach r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-promises r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 271 to remove and 0 not upgraded. After this operation, 1209 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 ... 58561 files and directories currently installed.) Removing r-bioc-titancna (1.42.0-1) ... Removing r-bioc-variantannotation (1.50.0-1) ... Removing r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Removing r-bioc-bsgenome (1.72.0-1) ... Removing r-bioc-biocstyle (2.32.1+dfsg-1) ... Removing texlive-bibtex-extra (2024.20241115-1) ... Removing r-cran-bookdown (0.41+dfsg-1) ... Removing r-cran-rmarkdown (2.28+dfsg-1) ... Removing r-cran-shiny (1.9.1+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-knitr (1.49+dfsg-1) ... Removing libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing texlive-latex-base (2024.20241115-1) ... Removing fonts-lmodern (2.005-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing r-cran-bslib (0.7.0+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (11+nmu1) ... Removing texlive-base (2024.20241115-1) ... Removing libbibtex-parser-perl (1.05+dfsg-1) ... Removing r-bioc-annotationdbi (1.66.0-1) ... Removing r-bioc-keggrest (1.44.1+dfsg-1) ... Removing liblatex-tounicode-perl (0.55-1) ... Removing r-cran-data.table (1.16.2+dfsg-1) ... Removing libio-string-perl (1.08-4) ... Removing libjs-d3 (3.5.17-4) ... Removing libjs-es5-shim (4.6.7-2) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-highlight.js (9.18.5+dfsg1-2) ... Removing r-cran-jquerylib (0.1.4+dfsg-4) ... Removing libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Removing libjs-jquery-datatables (1.11.5+dfsg-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-json (0~20221030+~1.0.8-1) ... Removing libjs-lunr (2.3.9~dfsg-2) ... Removing libjs-microplugin.js (0.0.3+dfsg-1.1) ... Removing libjs-modernizr (3.13.0-0.1) ... Removing libjs-prettify (2015.12.04+dfsg-1.1) ... Removing libjs-sifter.js (0.6.0+dfsg-3) ... Removing pandoc (3.1.11.1+ds-2) ... Removing liblua5.4-0:amd64 (5.4.7-1+b1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing r-cran-png (0.1-8-1+b1) ... Removing r-cran-httpuv (1.6.15+dfsg-1) ... Removing r-cran-sass (0.4.9+dfsg-1) ... Removing r-cran-fs (1.6.4+dfsg-1) ... Removing libuv1t64:amd64 (1.48.0-7) ... Removing libyaml-0-2:amd64 (0.2.5-1+b2) ... Removing r-cran-promises (1.3.0+dfsg-1) ... Removing r-cran-later (1.3.2+dfsg-1) ... Removing r-cran-rcpp (1.0.13-1-1) ... Removing littler (0.3.20-1) ... Removing node-bootstrap-sass (3.4.3-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing pandoc-data (3.1.11.1-3) ... Removing r-bioc-biocversion (3.19.1-1) ... Removing r-cran-fontawesome (0.5.2-1) ... Removing r-cran-htmltools (0.5.8.1-1) ... Removing r-cran-base64enc (0.1-3-3) ... Removing r-cran-biocmanager (1.30.25+dfsg-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-foreach (1.5.2-1) ... Removing r-cran-commonmark (1.9.2-1) ... Removing r-cran-dbi (1.2.3-1) ... 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-fastmap (1.2.0-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-iterators (1.0.14-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sourcetools (0.1.7-1-1) ... Removing r-cran-tinytex (0.53-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-withr (3.0.2+dfsg-1) ... Removing r-cran-xfun (0.49+dfsg-1) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-bioc-rtracklayer (1.64.0-1) ... Removing r-bioc-genomicalignments (1.40.0-1) ... Removing r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Removing r-bioc-delayedarray (0.30.1+dfsg-1) ... Removing r-bioc-sparsearray (1.4.8+dfsg-1) ... Removing r-bioc-s4arrays (1.4.1+dfsg-1) ... Removing r-cran-abind (1.4-8-1) ... Removing r-bioc-rsamtools (2.20.0+dfsg-1) ... Removing r-bioc-biocparallel (1.38.0-2) ... Removing r-cran-snow (1:0.4.4-2) ... Removing texlive-binaries (2024.20240313.70630+ds-5) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-3.2+b2) ... Removing libstdc++-14-dev:amd64 (14.2.0-8) ... Removing libgcc-14-dev:amd64 (14.2.0-8) ... Removing libasan8:amd64 (14.2.0-8) ... Removing r-bioc-genomicranges (1.56.2+dfsg-1) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing r-bioc-xvector (0.44.0-1) ... Removing r-bioc-rhtslib (3.0.0+dfsg-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libc6-dev:amd64 (2.40-4) ... Removing libc-dev-bin (2.40-4) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing tex-common (6.18) ... Removing libhwasan0:amd64 (14.2.0-8) ... Removing libxaw7:amd64 (2:1.0.16-1) ... Removing libxmu6:amd64 (2:1.1.3-3+b3) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libitm1:amd64 (14.2.0-8) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libptexenc1:amd64 (2024.20240313.70630+ds-5) ... Removing libkpathsea6:amd64 (2024.20240313.70630+ds-5) ... Removing liblsan0:amd64 (14.2.0-8) ... Removing libmpfi0:amd64 (1.5.4+ds-4) ... Removing libmpfr6:amd64 (4.2.1-1+b2) ... Removing libpotrace0:amd64 (1.16-2+b2) ... Removing libquadmath0:amd64 (14.2.0-8) ... Removing libsynctex2:amd64 (2024.20240313.70630+ds-5) ... Removing libteckit0:amd64 (2.5.12+ds1-1+b1) ... Removing libtexlua53-5:amd64 (2024.20240313.70630+ds-5) ... Removing libtsan2:amd64 (14.2.0-8) ... Removing libubsan1:amd64 (14.2.0-8) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxpm4:amd64 (1:3.5.17-1+b2) ... Removing libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Removing linux-libc-dev (6.12.3-1) ... Removing r-bioc-biobase (2.64.0-4) ... Removing r-bioc-biocio (1.14.0+dfsg-1) ... Removing r-bioc-matrixgenerics (1.16.0-2) ... Removing r-cran-rcurl (1.98-1.16+dfsg-1) ... Removing r-cran-bitops (1.0-8-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-cpp11 (0.5.0-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-2) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.8.0-1) ... Removing r-cran-matrixstats (1.4.1-1) ... Removing r-cran-rjson (0.2.23-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-yaml (2.3.10-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing t1utils (1.41-4) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Removing r-bioc-ucsc.utils (1.0.0+ds-2) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-curl (5.2.3+dfsg-1) ... Removing r-bioc-iranges (2.38.1-1) ... Removing r-bioc-s4vectors (0.42.1+dfsg-2) ... Removing r-bioc-biocgenerics (0.50.0-2) ... Removing r-bioc-genomeinfodbdata (1.2.12-1) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... Removing r-cran-askpass (1.2.1-1) ... Removing r-cran-cli (3.6.3-1) ... Removing r-cran-jsonlite (1.8.9+dfsg-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-sys (3.4.3-1) ... 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 (1.55.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.55.0+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 libharfbuzz0b:amd64 (10.1.0-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libcurl4t64:amd64 (8.11.0-1) ... 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 libfribidi0:amd64 (1.0.15-1) ... Removing libpaper-utils (1.1.29+b2) ... Removing libpaper1:amd64 (1.1.29+b2) ... Removing ucf (3.0045) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... 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 procps (2:4.0.4-6) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... 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 perl-modules-5.40 (5.40.0-8) ... Removing readline-common (8.2-5) ... 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 (1.2.1-2) ... Removing zip (3.0-14) ... 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 libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... 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 (1:1.1.5-1) ... Processing triggers for libc-bin (2.40-4) ... 1m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnuma1:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-promises', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-titancna'] 1m16.7s INFO: Running scripts post_remove 1m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_remove_exceptions'] 1m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_remove_exceptions'] 1m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnuma1:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-promises', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m17.0s DUMP: (Reading database ... 5216 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) ... Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-glyphicons-halflings which isn't installed Purging configuration files for fonts-lmodern (2.005-1) ... dpkg: warning: while removing fonts-lmodern, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-mathjax which isn't installed Purging configuration files for javascript-common (11+nmu1) ... dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbibtex-parser-perl which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 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 libhwasan0 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 libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed Purging configuration files for libjs-bootstrap4 (4.6.1+dfsg1-4) ... dpkg: warning: ignoring request to remove libjs-d3 which isn't installed dpkg: warning: ignoring request to remove libjs-es5-shim which isn't installed dpkg: warning: ignoring request to remove libjs-highlight.js which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-datatables which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-selectize.js which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-json which isn't installed dpkg: warning: ignoring request to remove libjs-lunr which isn't installed dpkg: warning: ignoring request to remove libjs-mathjax which isn't installed dpkg: warning: ignoring request to remove libjs-microplugin.js which isn't installed dpkg: warning: ignoring request to remove libjs-modernizr which isn't installed Purging configuration files for libjs-popper.js (1.16.1+ds-6) ... dpkg: warning: ignoring request to remove libjs-prettify which isn't installed dpkg: warning: ignoring request to remove libjs-sifter.js which isn't installed dpkg: warning: ignoring request to remove libjs-twitter-bootstrap-datepicker which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkpathsea6 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 liblatex-tounicode-perl which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblua5.4-0 which isn't installed dpkg: warning: ignoring request to remove libmpfi0 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnuma1 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 libperl5.40 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpotrace0 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libptexenc1 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... 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 libstdc++-14-dev which isn't installed dpkg: warning: ignoring request to remove libsynctex2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libteckit0 which isn't installed dpkg: warning: ignoring request to remove libtexlua53-5 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove 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 libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxaw7 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmu6 which isn't installed dpkg: warning: ignoring request to remove libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove libzzip-0-13t64 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove node-bootstrap-sass which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove node-normalize.css which isn't installed Purging configuration files for openssl (3.3.2-2) ... dpkg: warning: ignoring request to remove pandoc which isn't installed dpkg: warning: ignoring request to remove pandoc-data which isn't installed Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for procps (2:4.0.4-6) ... 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-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocstyle which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocversion which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-bsgenome which isn't installed dpkg: warning: ignoring request to remove r-bioc-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicalignments which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicfeatures which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-keggrest which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-variantannotation which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-base64enc which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-biocmanager which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-bookdown which isn't installed dpkg: warning: ignoring request to remove r-cran-bslib which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-commonmark which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-data.table which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-fontawesome which isn't installed dpkg: warning: ignoring request to remove r-cran-foreach which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-fs which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-generics which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-highr which isn't installed dpkg: warning: ignoring request to remove r-cran-htmltools which isn't installed dpkg: warning: ignoring request to remove r-cran-httpuv which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-iterators which isn't installed dpkg: warning: ignoring request to remove r-cran-jquerylib which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-knitr which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-later which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-promises which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rmarkdown which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-sass which isn't installed dpkg: warning: ignoring request to remove r-cran-shiny which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-sourcetools which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-tinytex which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xfun which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xtable which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove t1utils which isn't installed Purging configuration files for tex-common (6.18) ... Purging configuration files for texlive-base (2024.20241115-1) ... Purging configuration files for texlive-bibtex-extra (2024.20241115-1) ... dpkg: warning: ignoring request to remove texlive-binaries which isn't installed Purging configuration files for texlive-latex-base (2024.20241115-1) ... Purging configuration files for ucf (3.0045) ... 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 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnuma1:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-data.table', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-htmltools', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-iterators', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-promises', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', 'r-bioc-titancna'] 1m17.0s DUMP: dpkg: warning: ignoring request to remove r-bioc-titancna which isn't installed 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', 'r-bioc-titancna'] 1m17.0s INFO: Running scripts post_purge 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_purge_exceptions'] 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_purge_exceptions'] 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', '--pending'] 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--purge', '--pending'] 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--remove', '--pending'] 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg', '--remove', '--pending'] 1m17.0s INFO: Running scripts post_test 1m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_test_exceptions'] 1m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'tmp/scripts/post_test_exceptions'] 1m17.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m17.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-divert', '--list'] 1m17.2s 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 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'dpkg-divert', '--list'] 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'clean'] 1m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s', 'apt-get', 'clean'] 1m17.3s DEBUG: Recording chroot state 1m17.6s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fonts-lmodern, fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fonts-lmodern, 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 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/shm'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/shm'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/console'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/console'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/ptmx'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/ptmx'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/dev/pts'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/proc'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s/proc'] 1m17.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m17.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpp4vvfw8s'] 1m17.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpp4vvfw8s 1m17.9s INFO: PASS: Upgrading between Debian distributions. 1m17.9s INFO: PASS: All tests. 1m17.9s INFO: piuparts run ends. ret=0 End: 2024-12-07 15:14:23 GMT