Start: 2024-10-29 17:32:14 GMT Package: r-bioc-structuralvariantannotation Version: 1.20.0+ds-1 Installed-Size: 1297 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-genomicranges (>= 1.56.1), r-bioc-rtracklayer (>= 1.64.0), r-bioc-variantannotation (>= 1.50.0), r-bioc-biocgenerics (>= 0.50.0), r-cran-assertthat, r-bioc-biostrings (>= 2.72.1), r-bioc-pwalign (>= 1.0.0-2~0exp1), r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures (>= 1.56.0), r-bioc-iranges (>= 2.38.1), r-bioc-s4vectors (>= 0.42.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-genomeinfodb (>= 1.40.1) Suggests: r-cran-ggplot2, r-cran-devtools, r-cran-testthat (>= 2.1.0), r-cran-roxygen2, r-cran-rmarkdown, r-cran-tidyverse, r-cran-knitr, r-bioc-ggbio (>= 1.52.0), r-bioc-biovizbase (>= 1.52.0) Description: Variant annotations for structural variants Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Description-md5: da0d30e1c2fddfc05ec9f7a5a97d4001 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-structuralvariantannotation/r-bioc-structuralvariantannotation_1.20.0+ds-1_all.deb Size: 400596 MD5sum: 44d27862845fafc7f10bc0e95f1974dc SHA256: fab373bf705cad91e8e1677fd110be6885cb36784eed9d9c71777b8408f0b696 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-log-alternatives --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/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.20.0+ds-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-log-alternatives --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/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.20.0+ds-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnnpt72vc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnnpt72vc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpnnpt72vc/tmp/scripts/ 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnnpt72vc/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'update'] 0m1.9s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 81aee1340576354a215f8260e1283ddd - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_forbid_home'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'clean'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'clean'] 0m4.3s DEBUG: Recording chroot state 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-7 install ok installed gpgv gpgv 2.2.45-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-7 install ok installed libsystemd0:amd64 libsystemd0 256.7-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.7-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-divert', '--list'] 0m5.0s 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 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-divert', '--list'] 0m5.0s INFO: Running scripts is_testable 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/is_testable_uninstallable'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/is_testable_uninstallable'] 0m5.0s INFO: apt-cache does not know about any of the requested packages 0m5.0s INFO: Running scripts pre_test 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_test_exceptions'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 0m5.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 0m6.2s DEBUG: No broken symlinks as far as we can find. 0m6.2s INFO: Running scripts pre_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_database-server'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_extras'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_log_alternatives'] 0m6.3s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_install_log_alternatives'] 0m6.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 0m6.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 0m7.4s DEBUG: No broken symlinks as far as we can find. 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-cache', 'policy'] 0m8.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-cache', 'policy'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation'] 0m8.7s DUMP: r-bioc-structuralvariantannotation: Installed: (none) Candidate: 1.20.0+ds-1 Version table: 1.20.0+ds-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.20.0+ds-1'] 1m24.4s DUMP: Reading package lists... Building dependency tree... 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-pwalign r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome 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-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-stringi r-cran-stringr 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-foreach r-cran-bbmisc r-cran-doparallel r-bioc-shortread r-cran-batchtools r-cran-data.table 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-txdbmaker r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-cran-ggplot2 r-cran-devtools r-cran-roxygen2 r-cran-tidyverse r-bioc-ggbio r-bioc-biovizbase r-bioc-rhdf5 r-cran-rmariadb r-bioc-snpstats r-cran-magick r-cran-covr r-cran-ff r-cran-rstudioapi r-cran-rmysql r-cran-getopt r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-scales 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-broom r-cran-dbplyr r-cran-purrr r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-unitizer r-cran-rsvg r-cran-survival r-cran-pkgload r-cran-waldo r-cran-markdown 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-data.table r-cran-mockr r-cran-formattable 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-pwalign r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-structuralvariantannotation r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome 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-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-stringi r-cran-stringr 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, 269 newly installed, 0 to remove and 0 not upgraded. Need to get 375 MB of archives. After this operation, 1197 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-6 [3022 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-6 [4326 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-6 [267 kB] Get:6 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:9 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:10 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.3-2 [105 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:15 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:16 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:17 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:19 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:20 http://deb.debian.org/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:21 http://deb.debian.org/debian sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:22 http://deb.debian.org/debian sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:23 http://deb.debian.org/debian sid/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:24 http://deb.debian.org/debian sid/main amd64 javascript-common all 11+nmu1 [6260 B] Get:25 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-7 [2729 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-7 [9284 B] Get:27 http://deb.debian.org/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:28 http://deb.debian.org/debian sid/main amd64 liblatex-tounicode-perl all 0.55-1 [28.8 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libbibtex-parser-perl all 1.05+dfsg-1 [17.4 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-7 [137 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-7 [26.0 kB] Get:33 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-7 [1205 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-7 [2460 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-7 [1075 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-7 [1489 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-7 [145 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-7 [2673 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.11.5-1 [2443 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:42 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.40-3 [1956 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-7 [2368 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get:46 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:47 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:61 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:68 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.10.1-2 [352 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-7 [837 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:78 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:93 http://deb.debian.org/debian sid/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libjs-lunr all 2.3.9~dfsg-2 [76.6 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [157 kB] Get:102 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:103 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:104 http://deb.debian.org/debian sid/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:115 http://deb.debian.org/debian sid/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [49.1 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [62.5 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [114 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:140 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB] Get:141 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:142 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:143 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get:144 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:145 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-1 [16.0 kB] Get:146 http://deb.debian.org/debian sid/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:147 http://deb.debian.org/debian sid/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:148 http://deb.debian.org/debian sid/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:149 http://deb.debian.org/debian sid/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:150 http://deb.debian.org/debian sid/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get:151 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:152 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:153 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:154 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:155 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:156 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:157 http://deb.debian.org/debian sid/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:158 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:159 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:160 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:161 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:162 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:163 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:164 http://deb.debian.org/debian sid/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:165 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:166 http://deb.debian.org/debian sid/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:167 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:168 http://deb.debian.org/debian sid/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:169 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:170 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:171 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:172 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:173 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:174 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:178 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:179 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:180 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:181 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:182 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:183 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:184 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:185 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:186 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:187 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:188 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:189 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:190 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:191 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:192 http://deb.debian.org/debian sid/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:193 http://deb.debian.org/debian sid/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:194 http://deb.debian.org/debian sid/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:195 http://deb.debian.org/debian sid/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:196 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:197 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:198 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:199 http://deb.debian.org/debian sid/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:200 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:201 http://deb.debian.org/debian sid/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:202 http://deb.debian.org/debian sid/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get:203 http://deb.debian.org/debian sid/main amd64 r-cran-xfun amd64 0.48+dfsg-1 [544 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:205 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:206 http://deb.debian.org/debian sid/main amd64 r-cran-knitr all 1.48+dfsg-1 [912 kB] Get:207 http://deb.debian.org/debian sid/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:208 http://deb.debian.org/debian sid/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:209 http://deb.debian.org/debian sid/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:210 http://deb.debian.org/debian sid/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:211 http://deb.debian.org/debian sid/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:212 http://deb.debian.org/debian sid/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:213 http://deb.debian.org/debian sid/main amd64 r-cran-tinytex all 0.53-1 [146 kB] Get:214 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:215 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:216 http://deb.debian.org/debian sid/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:217 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:219 http://deb.debian.org/debian sid/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:220 http://deb.debian.org/debian sid/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:221 http://deb.debian.org/debian sid/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:222 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.1+dfsg-1 [226 kB] Get:223 http://deb.debian.org/debian sid/main amd64 r-cran-commonmark amd64 1.9.2-1 [122 kB] Get:224 http://deb.debian.org/debian sid/main amd64 r-cran-shiny all 1.9.1+dfsg-1 [3126 kB] Get:225 http://deb.debian.org/debian sid/main amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1474 kB] Get:226 http://deb.debian.org/debian sid/main amd64 r-cran-bookdown all 0.40+dfsg-1 [1404 kB] Get:227 http://deb.debian.org/debian sid/main amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] Get:228 http://deb.debian.org/debian sid/main amd64 tex-common all 6.18 [32.5 kB] Get:229 http://deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:230 http://deb.debian.org/debian sid/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8493 kB] Get:231 http://deb.debian.org/debian sid/main amd64 texlive-base all 2024.20240829-2 [22.7 MB] Get:232 http://deb.debian.org/debian sid/main amd64 texlive-latex-base all 2024.20240829-2 [1273 kB] Get:233 http://deb.debian.org/debian sid/main amd64 texlive-bibtex-extra all 2024.20240829-1 [79.9 MB] Get:234 http://deb.debian.org/debian sid/main amd64 r-bioc-biocversion all 3.19.1-1 [10.9 kB] Get:235 http://deb.debian.org/debian sid/main amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [453 kB] Get:236 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.2+dfsg-1 [1843 kB] Get:237 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:238 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.0-8-1 [30.7 kB] Get:239 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:240 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:241 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:242 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:243 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:244 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:245 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:246 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:247 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:248 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:249 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:250 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:251 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:252 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:253 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:254 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:255 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.72.0-1 [6812 kB] Get:256 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [918 kB] Get:257 http://deb.debian.org/debian sid/main amd64 r-bioc-pwalign amd64 1.0.0-2 [755 kB] Get:258 http://deb.debian.org/debian sid/main amd64 r-bioc-variantannotation amd64 1.50.0-1 [3508 kB] Get:259 http://deb.debian.org/debian sid/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:260 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get:261 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:262 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:263 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:264 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:265 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:266 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-bioc-structuralvariantannotation all 1.20.0+ds-1 [401 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 375 MB in 2s (168 MB/s) Selecting previously unselected package perl-modules-5.40. (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 .../000-perl-modules-5.40_5.40.0-6_all.deb ... Unpacking perl-modules-5.40 (5.40.0-6) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../001-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. 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Setting up zip (3.0-14) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libmpfr6:amd64 (4.2.1-1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up t1utils (1.41-4) ... Setting up libquadmath0:amd64 (14.2.0-7) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Setting up libjs-d3 (3.5.17-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-7) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-7) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libubsan1:amd64 (14.2.0-7) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... Setting up perl-modules-5.40 (5.40.0-6) ... Setting up sensible-utils (0.0.24) ... Setting up libhwasan0:amd64 (14.2.0-7) ... Setting up libcrypt-dev:amd64 (1:4.4.36-5) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libasan8:amd64 (14.2.0-7) ... Setting up fonts-lmodern (2.005-1) ... Setting up liblua5.4-0:amd64 (5.4.6-3+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libthai-data (0.1.29-2) ... Setting up node-bootstrap-sass (3.4.3-2) ... Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libjs-bootstrap4 (4.6.1+dfsg1-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up libtsan2:amd64 (14.2.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libc-dev-bin (2.40-3) ... Setting up openssl (3.3.2-2) ... Setting up node-normalize.css (8.0.1-5) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblsan0:amd64 (14.2.0-7) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libitm1:amd64 (14.2.0-7) ... Setting up libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libperl5.40:amd64 (5.40.0-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.40.0-6) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libc6-dev:amd64 (2.40-3) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libgcc-14-dev:amd64 (14.2.0-7) ... Setting up libstdc++-14-dev:amd64 (14.2.0-7) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.2) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.10.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up liblatex-tounicode-perl (0.55-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libio-string-perl (1.08-4) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up libbibtex-parser-perl (1.05+dfsg-1) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-xml (3.99-0.17-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up r-cran-commonmark (1.9.2-1) ... Setting up r-cran-rjson (0.2.23-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up texlive-base (2024.20240829-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.12-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.4+dfsg-1) ... Setting up r-cran-rcpp (1.0.13-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.20-1) ... Setting up r-bioc-matrixgenerics (1.16.0-2) ... Setting up r-cran-xfun (0.48+dfsg-1) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (3.0.1+dfsg-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-abind (1.4-8-1) ... Setting up r-cran-digest (0.6.37-1) ... Setting up r-cran-yaml (2.3.10-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-evaluate (1.0.0-1) ... Setting up r-cran-dbi (1.2.3-1) ... Setting up r-cran-highr (0.11+dfsg-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bitops (1.0-8-1) ... Setting up r-bioc-biocversion (3.19.1-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-cran-biocmanager (1.30.25+dfsg-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-cran-fastmap (1.2.0-1) ... Setting up r-cran-png (0.1-8-1+b1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up r-cran-jsonlite (1.8.9+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.4-1) ... Setting up texlive-latex-base (2024.20240829-2) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-later (1.3.2+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-htmltools (0.5.8.1-1) ... Setting up r-cran-tinytex (0.53-1) ... Setting up r-cran-knitr (1.48+dfsg-1) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up texlive-bibtex-extra (2024.20240829-1) ... 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 (1.1.4-1) ... 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 (1.56.2+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 (0.40+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-bioc-pwalign (1.0.0-2) ... 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-structuralvariantannotation (1.20.0+ds-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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. 1m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.20.0+ds-1'] 1m24.4s INFO: Running scripts post_install 1m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_install_exceptions'] 1m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_install_exceptions'] 1m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_install_log_alternatives'] 1m24.4s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=libblas3: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=xdg-utils: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --install /usr/bin/open open /usr/bin/xdg-open 50 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/xdg-open.1.gz LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=perl: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=texlive-binaries: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --install /usr/bin/xdvi.bin xdvi.bin /usr/bin/xdvi-xaw 30 LOG-ALTERNATIVES: dpkg=texlive-binaries: piuparts=r-bioc-structuralvariantannotation=1.20.0+ds-1: /usr/bin/update-alternatives --install /usr/bin/bibtex bibtex /usr/bin/bibtex.original 100 --slave /usr/share/man/man1/bibtex.1.gz bibtex.1.gz /usr/share/man/man1/bibtex.original.1.gz 1m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_install_log_alternatives'] 1m24.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 1m26.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 1m33.9s DEBUG: No broken symlinks as far as we can find. 1m38.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '-ac', '--ignore-obsolete'] 1m43.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '-ac', '--ignore-obsolete'] 1m43.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m43.8s DUMP: 0.15.6 1m43.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m43.8s INFO: Running adequate version 0.15.6 now. 1m43.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'r-bioc-structuralvariantannotation'] 1m43.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'r-bioc-structuralvariantannotation'] 1m43.9s INFO: Running scripts pre_remove 1m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m44.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m44.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m44.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m44.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m53.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m53.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m53.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m53.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_exceptions'] 1m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/pre_remove_exceptions'] 1m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m53.2s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1+b1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-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 14.2.0-7 install ok installed gpgv gpgv 2.2.45-1 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 2.9.10 install ok installed libasan8:amd64 libasan8 14.2.0-7 install ok installed libatomic1:amd64 libatomic1 14.2.0-7 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libbibtex-parser-perl libbibtex-parser-perl 1.05+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 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 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc-dev-bin libc-dev-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libc6-dev:amd64 libc6-dev 2.40-3 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl4t64:amd64 libcurl4t64 8.10.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272+b1 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.3-2 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-7 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-7 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 14.2.0-7 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-7 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-7 install ok installed libice6:amd64 libice6 2:1.0.10-1+b1 install ok installed libicu72:amd64 libicu72 72.1-5 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libitm1:amd64 libitm1 14.2.0-7 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-4 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-es5-shim libjs-es5-shim 4.6.7-2 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-jquery-selectize.js libjs-jquery-selectize.js 0.12.6+dfsg-1.1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-json libjs-json 0~20221030+~1.0.8-1 install ok installed libjs-lunr libjs-lunr 2.3.9~dfsg-2 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libjs-microplugin.js libjs-microplugin.js 0.0.3+dfsg-1.1 install ok installed libjs-modernizr libjs-modernizr 3.13.0-0.1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-6 install ok installed libjs-prettify libjs-prettify 2015.12.04+dfsg-1.1 install ok installed libjs-sifter.js libjs-sifter.js 0.6.0+dfsg-3 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkpathsea6:amd64 libkpathsea6 2024.20240313.70630+ds-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblatex-tounicode-perl liblatex-tounicode-perl 0.55-1 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-4+b1 install ok installed liblsan0:amd64 liblsan0 14.2.0-7 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.6-3+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.3-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libmpfi0:amd64 libmpfi0 1.5.4+ds-3 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.63.0-1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-3 install ok installed libpaper-utils libpaper-utils 1.1.29+b1 install ok installed libpaper1:amd64 libpaper1 1.1.29+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-6 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libpotrace0:amd64 libpotrace0 1.16-2+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libptexenc1:amd64 libptexenc1 2024.20240313.70630+ds-4 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-7 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-7 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-7 install ok installed libsynctex2:amd64 libsynctex2 2024.20240313.70630+ds-4 install ok installed libsystemd0:amd64 libsystemd0 256.7-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libteckit0:amd64 libteckit0 2.5.12+ds1-1 install ok installed libtexlua53-5:amd64 libtexlua53-5 2024.20240313.70630+ds-4 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-7 install ok installed libubsan1:amd64 libubsan1 14.2.0-7 install ok installed libudev1:amd64 libudev1 256.7-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-6 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxaw7:amd64 libxaw7 2:1.0.14-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.1 install ok installed libxmu6:amd64 libxmu6 2:1.1.3-3+b2 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed libzzip-0-13t64:amd64 libzzip-0-13t64 0.13.72+dfsg.1-1.3 install ok installed linux-libc-dev linux-libc-dev 6.11.5-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 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 1:4.16.0-4 install ok installed perl perl 5.40.0-6 install ok installed perl-base perl-base 5.40.0-6 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-6 install ok installed r-base-core r-base-core 4.4.1-3 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-pwalign r-bioc-pwalign 1.0.0-2 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-structuralvariantannotation r-bioc-structuralvariantannotation 1.20.0+ds-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.34.0+dfsg-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-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-biocmanager r-cran-biocmanager 1.30.25+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 0.40+dfsg-1 install ok installed r-cran-bslib r-cran-bslib 0.7.0+dfsg-1 install ok installed r-cran-cachem r-cran-cachem 1.1.0-1 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-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 1.1.4-1 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-formatr r-cran-formatr 1.14-2 install ok installed r-cran-fs r-cran-fs 1.6.4+dfsg-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-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-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 1.48+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 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-stringi r-cran-stringi 1.8.4-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-sys r-cran-sys 3.4.3-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-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 3.0.1+dfsg-1 install ok installed r-cran-xfun r-cran-xfun 0.48+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 2024.20240829-2 install ok installed texlive-bibtex-extra texlive-bibtex-extra 2024.20240829-1 install ok installed texlive-binaries texlive-binaries 2024.20240313.70630+ds-4 install ok installed texlive-latex-base texlive-latex-base 2024.20240829-2 install ok installed tzdata tzdata 2024b-3 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1 1m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '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', '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', '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', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', '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-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-stringi', 'r-cran-stringr', '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-structuralvariantannotation'] 1m58.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-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-pwalign r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-structuralvariantannotation r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-fontawesome 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-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-stringi r-cran-stringr 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, 269 to remove and 0 not upgraded. After this operation, 1197 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 ... 58304 files and directories currently installed.) Removing r-bioc-structuralvariantannotation (1.20.0+ds-1) ... Removing r-bioc-variantannotation (1.50.0-1) ... Removing r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Removing r-bioc-bsgenome (1.72.0-1) ... Removing r-bioc-biocstyle (2.32.1+dfsg-1) ... Removing r-cran-bookdown (0.40+dfsg-1) ... Removing r-cran-rmarkdown (2.28+dfsg-1) ... Removing r-cran-shiny (1.9.1+dfsg-1) ... Removing texlive-bibtex-extra (2024.20240829-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-knitr (1.48+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 (2024.20240829-2) ... 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 (2024.20240829-2) ... Removing libbibtex-parser-perl (1.05+dfsg-1) ... Removing r-bioc-pwalign (1.0.0-2) ... 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 libio-string-perl (1.08-4) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.4-1) ... 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 (5.4.6-3+b1) ... Removing libnuma1:amd64 (2.0.18-1) ... 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 (1.48.0-6) ... Removing libyaml-0-2:amd64 (0.2.5-1+b1) ... Removing littler (0.3.20-1) ... Removing node-bootstrap-sass (3.4.3-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing pandoc-data (3.1.11.1-3) ... Removing r-bioc-biocversion (3.19.1-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-fontawesome (0.5.2-1) ... Removing r-cran-htmltools (0.5.8.1-1) ... Removing r-cran-base64enc (0.1-3-3) ... Removing r-cran-biocmanager (1.30.25+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 (1.1.4-1) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-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-generics (0.1.3-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... 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 (3.0.1+dfsg-1) ... Removing r-cran-xfun (0.48+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 r-cran-promises (1.3.0+dfsg-1) ... Removing texlive-binaries (2024.20240313.70630+ds-4) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-3.2) ... Removing libstdc++-14-dev:amd64 (14.2.0-7) ... Removing libgcc-14-dev:amd64 (14.2.0-7) ... Removing libasan8:amd64 (14.2.0-7) ... Removing r-bioc-genomicranges (1.56.2+dfsg-1) ... Removing r-bioc-rhtslib (3.0.0+dfsg-1) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing perl (5.40.0-6) ... Removing libperl5.40:amd64 (5.40.0-6) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libhwasan0:amd64 (14.2.0-7) ... Removing libxaw7:amd64 (2:1.0.14-1+b2) ... Removing libxmu6:amd64 (2:1.1.3-3+b2) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Removing libitm1:amd64 (14.2.0-7) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Removing libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Removing liblsan0:amd64 (14.2.0-7) ... Removing libmpfi0:amd64 (1.5.4+ds-3) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libpotrace0:amd64 (1.16-2+b1) ... Removing libquadmath0:amd64 (14.2.0-7) ... Removing libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Removing libteckit0:amd64 (2.5.12+ds1-1) ... Removing libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Removing libtsan2:amd64 (14.2.0-7) ... Removing libubsan1:amd64 (14.2.0-7) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxpm4:amd64 (1:3.5.17-1+b1) ... Removing libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Removing perl-modules-5.40 (5.40.0-6) ... 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-fastmap (1.2.0-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-2) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-later (1.3.2+dfsg-1) ... Removing r-cran-magrittr (2.0.3-1) ... 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 tex-common (6.18) ... Removing t1utils (1.41-4) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-cran-rcpp (1.0.13-1) ... 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-xvector (0.44.0-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Removing libc6-dev:amd64 (2.40-3) ... Removing libc-dev-bin (2.40-3) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing linux-libc-dev (6.11.5-1) ... 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-littler (0.3.20-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-sys (3.4.3-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-base-core (4.4.1-3) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-3) ... Removing fontconfig (2.15.0-1.1+b1) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-2) ... Removing libatomic1:amd64 (14.2.0-7) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libcurl4t64:amd64 (8.10.1-2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgfortran5:amd64 (14.2.0-7) ... Removing libgomp1:amd64 (14.2.0-7) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... 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) ... Removing libsm6:amd64 (2:1.2.3-1+b1) ... Removing libice6:amd64 (2:1.0.10-1+b1) ... Removing libicu72:amd64 (72.1-5) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing 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-4+b1) ... Removing libnghttp2-14:amd64 (1.63.0-1) ... Removing libpaper-utils (1.1.29+b1) ... Removing libpaper1:amd64 (1.1.29+b1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-5) ... 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+b4) ... 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) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... 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+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing openssl (3.3.2-2) ... Removing readline-common (8.2-5) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing 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+b5) ... Removing libexpat1:amd64 (2.6.3-2) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Processing triggers for libc-bin (2.40-3) ... 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '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', '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', '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', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', '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-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-stringi', 'r-cran-stringr', '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-structuralvariantannotation'] 1m58.4s INFO: Running scripts post_remove 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_remove_exceptions'] 1m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_remove_exceptions'] 1m58.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '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', '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', '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', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', '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-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-stringi', 'r-cran-stringr', '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'] 1m59.2s DUMP: (Reading database ... 5213 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 (2.82.2-2) ... 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 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+b1) ... 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 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) ... 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 (5.40.0-6) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for r-base-core (4.4.1-3) ... 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-pwalign which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-variantannotation which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-base64enc which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-biocmanager which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-bookdown which isn't installed dpkg: warning: ignoring request to remove r-cran-bslib which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-commonmark which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-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-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-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-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-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 (2024.20240829-2) ... Purging configuration files for texlive-bibtex-extra (2024.20240829-1) ... dpkg: warning: ignoring request to remove texlive-binaries which isn't installed Purging configuration files for texlive-latex-base (2024.20240829-2) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', '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', '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', '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', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-fontawesome', '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-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-stringi', 'r-cran-stringr', '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'] 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation'] 1m59.2s DUMP: dpkg: warning: ignoring request to remove r-bioc-structuralvariantannotation which isn't installed 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation'] 1m59.2s INFO: Running scripts post_purge 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_purge_exceptions'] 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_purge_exceptions'] 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--purge', '--pending'] 1m59.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--purge', '--pending'] 1m59.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--remove', '--pending'] 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg', '--remove', '--pending'] 1m59.3s INFO: Running scripts post_test 1m59.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_test_exceptions'] 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'tmp/scripts/post_test_exceptions'] 1m59.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 1m59.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 2m0.5s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf 2m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-divert', '--list'] 2m0.5s 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 2m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'dpkg-divert', '--list'] 2m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'clean'] 2m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc', 'apt-get', 'clean'] 2m0.6s DEBUG: Recording chroot state 2m1.4s 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 2m1.4s INFO: PASS: Installation and purging test. 2m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/shm'] 2m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/shm'] 2m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/console'] 2m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/console'] 2m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/ptmx'] 2m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/ptmx'] 2m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts'] 2m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/dev/pts'] 2m1.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/proc'] 2m1.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc/proc'] 2m1.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 2m2.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnnpt72vc'] 2m2.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnnpt72vc 2m2.0s INFO: PASS: All tests. 2m2.0s INFO: piuparts run ends. ret=0 End: 2024-10-29 17:34:16 GMT