Start: 2026-08-12 05:19:31 GMT [stable] Package: r-bioc-ballgown Version: 2.38.0+dfsg-2 Installed-Size: 4502 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-genomicranges (>= 1.17.25), r-bioc-iranges (>= 1.99.22), r-bioc-s4vectors (>= 0.9.39), r-cran-rcolorbrewer, r-bioc-sva, r-bioc-limma, r-bioc-rtracklayer (>= 1.29.25), r-bioc-biobase (>= 2.25.0), r-bioc-genomeinfodb Suggests: r-cran-testthat, r-cran-knitr, r-cran-markdown Description: Flexible, isoform-level differential expression analysis Homepage: https://bioconductor.org/packages/ballgown/ Description-md5: f4ae5d7c8c9bcfa4c48b5e78d093a9f0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-ballgown/r-bioc-ballgown_2.38.0+dfsg-2_all.deb Size: 2929864 MD5sum: 0483cedccee596a214669a0c615f405b SHA256: f952f7a609a998d4619eaee3b56497c553d2c667a4fed046ea847fc15096a4c2 [sid] Package: r-bioc-ballgown Version: 2.43.0+dfsg-1 Installed-Size: 4503 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-RELEASE, r-bioc-genomicranges (>= 1.17.25), r-bioc-iranges (>= 1.99.22), r-bioc-s4vectors (>= 0.9.39), r-cran-rcolorbrewer, r-bioc-sva, r-bioc-limma, r-bioc-rtracklayer (>= 1.29.25), r-bioc-biobase (>= 2.25.0), r-bioc-seqinfo, r-pkg-team-core-architecture Suggests: r-cran-testthat, r-cran-knitr, r-cran-markdown Description: Flexible, isoform-level differential expression analysis Homepage: https://bioconductor.org/packages/ballgown/ Description-md5: f4ae5d7c8c9bcfa4c48b5e78d093a9f0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-ballgown/r-bioc-ballgown_2.43.0+dfsg-1_all.deb Size: 2922180 MD5sum: a09e750608e51ab718094f0ac2aa41be SHA256: 2aa600fe90cc7fce22c727201eff0dcd9d24c6920e3ae3be41a5da067855d9aa Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt r-bioc-ballgown=2.43.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508211944~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt r-bioc-ballgown=2.43.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-52-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.180-1 (2026-08-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp9604zi98 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp9604zi98 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9604zi98', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9604zi98', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9604zi98/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9604zi98/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp9604zi98/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', 'update'] 0m1.1s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Reading package lists... 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', 'update'] 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 3f92b7cc74caef5cede49a389a4e0ed1 - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s 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 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s 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' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8+deb13u6 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b9 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.22 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69~deb13u1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 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 2.41-12+deb13u3 install ok installed libc6:amd64 libc6 2.41-12+deb13u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+deb13u1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1+deb13u1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1~deb13u1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7+deb13u1 install ok installed libssl3t64:amd64 libssl3t64 3.5.6-1~deb13u2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.13-1~deb13u1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.13-1~deb13u1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.6-1~deb13u2 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2+deb13u1 install ok installed sqv sqv 1.3.0-3+b2 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2026b-0+deb13u1 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 0m3.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 0m3.2s INFO: Running scripts is_testable 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s INFO: Running scripts pre_test 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_test_root_password'] 0m3.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_test_root_password'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-ballgown'] 0m3.5s DUMP: Package: r-bioc-ballgown Version: 2.38.0+dfsg-2 Installed-Size: 4502 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-genomicranges (>= 1.17.25), r-bioc-iranges (>= 1.99.22), r-bioc-s4vectors (>= 0.9.39), r-cran-rcolorbrewer, r-bioc-sva, r-bioc-limma, r-bioc-rtracklayer (>= 1.29.25), r-bioc-biobase (>= 2.25.0), r-bioc-genomeinfodb Suggests: r-cran-testthat, r-cran-knitr, r-cran-markdown Description-en: Flexible, isoform-level differential expression analysis Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. Description-md5: f4ae5d7c8c9bcfa4c48b5e78d093a9f0 Homepage: https://bioconductor.org/packages/ballgown/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-ballgown/r-bioc-ballgown_2.38.0+dfsg-2_all.deb Size: 2929864 MD5sum: 0483cedccee596a214669a0c615f405b SHA256: f952f7a609a998d4619eaee3b56497c553d2c667a4fed046ea847fc15096a4c2 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-ballgown'] 0m3.5s INFO: apt-cache knows about the following packages: r-bioc-ballgown 0m3.5s INFO: Running scripts pre_install 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_database-server'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_extras'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy'] 0m3.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.6,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy', 'r-bioc-ballgown'] 0m3.6s DUMP: r-bioc-ballgown: Installed: (none) Candidate: 2.38.0+dfsg-2 Version table: 2.38.0+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy', 'r-bioc-ballgown'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-y', 'install', 'r-bioc-ballgown'] 0m23.5s 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 libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcolorbrewer r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: 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 low-memory-monitor gnutls-bin krb5-doc krb5-user libstdc++-14-doc tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-go.db r-bioc-org.hs.eg.db r-cran-runit r-bioc-biocstyle r-cran-knitr r-bioc-graph r-cran-testthat r-cran-markdown r-bioc-all r-bioc-golubesets r-bioc-hdf5array r-bioc-pwalign r-bioc-affy r-bioc-deseq2 r-cran-rmarkdown r-cran-foreach r-cran-bbmisc r-cran-doparallel r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-cran-data.table r-bioc-bsgenome r-bioc-genomicfeatures r-cran-covr r-cran-lobstr r-bioc-delayedmatrixstats r-cran-readr r-bioc-rhdf5 r-cran-seuratobject r-cran-class r-cran-r.utils r-bioc-txdbmaker r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-cran-digest r-cran-biasedurn r-cran-ellipse r-cran-gplots r-cran-mass r-bioc-sparsematrixstats r-bioc-experimenthub r-bioc-singlecellexperiment r-bioc-bladderbatch r-cran-rmariadb r-cran-pillar r-cran-rmysql r-cran-interp r-cran-gam r-cran-rcpp r-cran-rmpi r-cran-rlecuyer r-cran-plm r-cran-zoo readline-doc Recommended packages: manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-roxygen2 r-cran-knitr r-cran-markdown r-cran-rmarkdown r-cran-ff r-cran-microbenchmark r-cran-withr r-cran-callr r-cran-covr r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-processx r-cran-ps r-cran-rprojroot r-cran-rstudioapi r-cran-tibble r-cran-whoami r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-ggplot2 r-cran-lobstr r-cran-mockery r-cran-progress r-cran-scales r-cran-rcpp r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-shiny r-cran-testit r-cran-dplyr r-cran-magrittr r-cran-waldo r-cran-jpeg r-cran-readr r-cran-xml2 r-cran-r.rsp r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-r.devices r-cran-sodium r-cran-runit r-cran-fs r-cran-pillar r-cran-usethis r-cran-dbitest r-cran-gert r-cran-gh r-cran-hms r-cran-rvest r-cran-generics r-cran-pkgdown r-cran-zeallot 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 libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-ballgown r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcolorbrewer r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 189 newly installed, 0 to remove and 0 not upgraded. Need to get 204 MB of archives. After this operation, 582 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.5.6-1~deb13u2 [1503 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20250419 [162 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:10 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:11 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0052 [43.3 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1+deb13u5 [283 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1+deb13u1 [452 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:22 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-6 [160 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.41-12+deb13u3 [59.8 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.12.94-1 [2848 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.41-12+deb13u3 [1992 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get:38 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:39 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b11 [25.0 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5+deb13u1 [33.1 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5+deb13u1 [81.2 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:54 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5+deb13u1 [326 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5+deb13u1 [138 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1+deb13u1 [76.2 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2+deb13u1 [50.1 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3+deb13u4 [1469 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1+deb13u1 [245 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2+deb13u4 [392 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.4-3~deb13u3 [1519 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+deb13u1 [75.2 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+deb13u1 [479 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24+deb13u1 [217 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-6 [2447 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3+deb13u2 [345 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1+deb13u3 [700 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-15 [235 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-29 [173 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.5.0-3 [28.6 MB] Get:109 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.40.1-3 [2310 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.6.0+dfsg-1 [455 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.6.0-1-4 [489 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.5-3 [1709 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.4-1 [1370 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.2-1 [226 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.9-1 [1216 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 6.2.1+dfsg-1 [195 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [445 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [402 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.6.1-1 [106 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B] Get:140 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] Get:143 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3848 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.3-1 [165 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.4 MB] Get:146 http://deb.debian.org/debian trixie/main amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [190 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotationdbi all 1.68.0-2 [4703 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.18-1 [1762 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1865 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2092 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-7-1 [1418 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.168-1 [2329 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-3-1 [4048 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-3-1 [3378 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.5.0-1 [502 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.18.1-1 [449 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.8-3-1 [8265 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-bioc-genefilter amd64 1.88.0-2 [1233 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:168 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.40.0-2 [1326 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-bioc-limma amd64 3.62.2+dfsg-1 [2023 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-locfit amd64 1.5-9.12-1 [513 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-bioc-edger amd64 4.4.2+dfsg-1 [1118 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-bioc-sva amd64 3.54.0-2 [455 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-bitops amd64 1.0-9-1 [30.7 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1335 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3600 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [702 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1372 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2076 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1116 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2161 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocio all 1.16.0+dfsg-2 [210 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 r-bioc-rtracklayer amd64 1.66.0-3 [5219 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 r-bioc-ballgown all 2.38.0+dfsg-2 [2930 kB] Preconfiguring packages ... Fetched 204 MB in 1s (161 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4940 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../001-libncursesw6_6.5+20250216-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-2) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../092-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../093-libsm6_2%3a1.2.6-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.6-1) ... Selecting previously unselected package libtcl8.6:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../099-libxft2_2.3.6-1+b4_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../100-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../101-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../102-libxml2_2.12.7+dfsg+really2.9.14-2.1+deb13u3_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1+deb13u3) ... 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Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.46.0-2) ... Setting up r-cran-rsqlite (2.3.9-1) ... Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ... Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ... Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... Setting up r-bioc-keggrest (1.46.0+dfsg-3) ... Setting up r-bioc-annotationdbi (1.68.0-2) ... Setting up r-bioc-annotate (1.84.0+dfsg-2) ... Setting up r-bioc-genefilter (1.88.0-2) ... Setting up r-bioc-genomicalignments (1.42.0-2) ... Setting up r-bioc-rtracklayer (1.66.0-3) ... Setting up r-bioc-sva (3.54.0-2) ... Setting up r-bioc-ballgown (2.38.0+dfsg-2) ... Processing triggers for libc-bin (2.41-12+deb13u3) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-y', 'install', 'r-bioc-ballgown'] 0m23.5s INFO: Running scripts post_install 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 0m24.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 0m24.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp9604zi98 to sid 0m24.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m24.9s INFO: Running scripts pre_distupgrade 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', 'update'] 0m27.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [193 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.7 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7703 kB] Fetched 18.6 MB in 2s (9080 kB/s) Reading package lists... 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', 'update'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-yf', 'dist-upgrade'] 1m6.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gcc-15-base libasan8 libatomic1 libblas3 libboost-dev libboost1.90-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgcc-15-dev libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu76 libicu78 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libproc2-1 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libstdc++-15-dev libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxml2-16 libxrender1 libxss1 libxt6t64 linux-libc-dev procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-cigarillo r-bioc-delayedarray r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-seqinfo r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-cran-abind r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcolorbrewer r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable r-cran-yaml r-pkg-team-core-architecture readline-common rpcsvc-proto ucf unzip x11-common xdg-utils zip zlib1g-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libboost1.83-dev r-bioc-ballgown r-bioc-zlibbioc The following NEW packages will be installed: gcc-15-base gcc-16-base libboost1.90-dev libc-gconv-modules-extra libgcc-15-dev libicu78 libngtcp2-16 libngtcp2-crypto-ossl0 libproc2-1 libstdc++-15-dev libxml2-16 r-bioc-cigarillo r-bioc-seqinfo r-cran-generics r-pkg-team-core-architecture The following packages will be upgraded: apt base-files base-passwd bash bsdutils ca-certificates coreutils debconf diffutils dpkg findutils fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gcc-14-base grep init-system-helpers libacl1 libapt-pkg7.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcom-err2 libcrypt-dev libcrypt1 libcurl4t64 libdatrie1 libdb5.3t64 libdebconfclient0 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgcc-s1 libgfortran5 libglib2.0-0t64 libgmp10 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed6t64 libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblastlog2-2 libldap2 liblerc4 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libncursesw6 libnettle8t64 libnghttp2-14 libnghttp3-9 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-8-0 libpixman-1-0 libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsharpyuv0 libsm6 libsmartcols1 libsqlite3-0 libssh2-1t64 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libudev1 libunistring5 libuuid1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libxxhash0 libzstd1 linux-libc-dev login login.defs mawk mount ncurses-base ncurses-bin openssl openssl-provider-legacy passwd perl-base procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcolorbrewer r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sed sensible-utils sqv sysvinit-utils tar tzdata ucf unzip util-linux x11-common zip zlib1g zlib1g-dev 254 upgraded, 15 newly installed, 3 to remove and 0 not upgraded. Need to get 251 MB of archives. After this operation, 96.3 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.4-1 [63.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.43-3 [38.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.5.2+20251210-1 [100 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.5.2+20251210-1 [130 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.43-3 [2067 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-gconv-modules-extra amd64 2.43-3 [1097 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.43-3 [1864 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.43-3 [620 kB] Get:9 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 7.1.7-1 [2038 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-16-base amd64 16.2.0-1 [38.0 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 16.2.0-1 [74.1 kB] Get:12 http://deb.debian.org/debian sid/main amd64 base-files amd64 14.2 [88.0 kB] Get:13 http://deb.debian.org/debian sid/main amd64 bash amd64 5.3-3 [1559 kB] Get:14 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.10-1 [3142 kB] Get:15 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.12-1 [405 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-6+b2 [39.9 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2+b2 [27.1 kB] Get:18 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.10.0-10 [70.3 kB] Get:19 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.8.3-1 [332 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.6.3-1 [2488 kB] Get:21 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.6.3-1 [320 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.7+dfsg-4 [304 kB] Get:23 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:24 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.2-3 [90.9 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 16.2.0-1 [824 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 261.2-1 [468 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 261.2-1 [140 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.3.2 [1229 kB] Get:29 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-5 [825 kB] Get:30 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.23.7 [1531 kB] Get:31 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.11.0-2 [782 kB] Get:32 http://deb.debian.org/debian sid/main amd64 grep amd64 3.12-1 [443 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.6+20260608-2 [137 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.6+20260608-2 [353 kB] Get:35 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.6+20260608-2 [445 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-12+b1 [9344 B] Get:37 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.42.2-3 [1852 kB] Get:38 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-3 [331 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.42.2-2 [33.6 kB] Get:40 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.42.2-2 [91.0 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.42.2-2 [173 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.42.2-2 [215 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.42.2-2 [145 kB] Get:44 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.42.2-2 [1230 kB] Get:45 http://deb.debian.org/debian sid/main amd64 mount amd64 2.42.2-2 [165 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.46-1+b2 [297 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.11-2 [87.3 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.283 [7572 B] Get:49 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5+b2 [560 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10.2-1+b1 [305 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10.2-1+b1 [335 kB] Get:53 http://deb.debian.org/debian sid/main amd64 sqv amd64 1.4.0-1 [683 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.6.1-1 [49.9 kB] Get:55 http://deb.debian.org/debian sid/main amd64 apt amd64 3.3.2 [1529 kB] Get:56 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.69+nmu1 [37.1 kB] Get:57 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.6+20260608-2 [276 kB] Get:58 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.18-1 [29.7 kB] Get:59 http://deb.debian.org/debian sid/main amd64 gcc-15-base amd64 15.3.0-2 [37.7 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 16.2.0-1 [151 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 16.2.0-1 [27.0 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 16.2.0-1 [10.4 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 16.2.0-1 [2889 kB] Get:64 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 16.2.0-1 [1280 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 16.2.0-1 [1136 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 16.2.0-1 [148 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 16.2.0-1 [1580 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 16.2.0-1 [878 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.4.0-1 [2682 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.4.0-1 [2674 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 16.2.0-1 [2573 kB] Get:72 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.4.0-1 [34.9 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libgcc-15-dev amd64 15.3.0-2 [2717 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libstdc++-15-dev amd64 15.3.0-2 [2784 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.90.0.2 [3064 B] Get:76 http://deb.debian.org/debian sid/main amd64 libboost1.90-dev amd64 1.90.0-6 [11.3 MB] Get:77 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.6-1 [1391 kB] Get:78 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.8.1-2 [172 kB] Get:79 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] Get:80 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.7.3-2 [1983 kB] Get:81 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.12-2 [120 kB] Get:82 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.3.0-1 [1742 kB] Get:83 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.6.1-4 [28.4 MB] Get:84 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-16 [239 kB] Get:85 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-31 [176 kB] Get:86 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.92 [123 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libpaper2 amd64 2.2.5-0.4 [16.6 kB] Get:88 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 2.2.5-0.4 [15.8 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-8 [206 kB] Get:91 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-9 [488 kB] Get:92 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-9 [840 kB] Get:93 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.8.3-1 [127 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.58-1 [289 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.14.3+dfsg-2 [492 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.46.4-1+b2 [259 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1+b2 [27.7 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-3+b1 [543 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.17.0-1 [68.1 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:118 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.4.2-1 [480 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.8-5 [109 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11+b1 [709 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-11 [17.2 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-11 [55.2 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.14+dfsg-1 [200 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-ossl0 amd64 1.24.0-1 [26.5 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.23.2-1 [61.6 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-5 [245 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.7.1-2 [30.5 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.88.3-2 [1536 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libicu78 amd64 78.3-2 [10.0 MB] Get:133 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB] Get:134 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-8 [2548 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.15-2 [75.8 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 12.3.2-2+b2 [513 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.58.0-1 [34.2 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.58.0-1 [53.1 kB] Get:139 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.17.1-5 [191 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-5+b1 [26.2 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.30-3 [172 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.14-2 [39.1 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.30-3 [51.7 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.58.0-1 [225 kB] Get:145 http://deb.debian.org/debian sid/main amd64 readline-common all 8.3-4 [74.8 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Get:147 http://deb.debian.org/debian sid/main amd64 tzdata all 2026c-1 [260 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.18+dfsg-1 [1053 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB] Get:150 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.2.0+ds-1 [203 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b2 [115 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1+b2 [335 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.2-1 [383 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.7+ds-1 [10.0 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.7+ds-1 [82.9 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b5 [54.8 kB] Get:157 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+26 [217 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b4 [17.0 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.18-1 [801 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1+b2 [66.8 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.6-1+b2 [37.9 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b2 [191 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-11 [7788 B] Get:164 http://deb.debian.org/debian sid/main amd64 libproc2-1 amd64 2:4.0.6-3 [69.4 kB] Get:165 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.6-3 [983 kB] Get:166 http://deb.debian.org/debian sid/main amd64 ucf all 3.0056 [47.1 kB] Get:167 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.6.3-1 [1522 kB] Get:168 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20260601 [134 kB] Get:169 http://deb.debian.org/debian sid/main amd64 r-pkg-team-core-architecture amd64 20260707 [4764 B] Get:170 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.50.1+dfsg-1 [1849 kB] Get:171 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.46.0-1 [2336 kB] Get:172 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.52.0-1 [629 kB] Get:173 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 7.1.0+dfsg-2 [203 kB] Get:174 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 2.0.0+dfsg-2 [447 kB] Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.13-2 [47.5 kB] Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.3-3 [44.4 kB] Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.1-3 [24.5 kB] Get:178 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.4.2+dfsg-1 [402 kB] Get:179 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.6.1-2 [106 kB] Get:180 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.8+dfsg-1 [471 kB] Get:181 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.8.0+dfsg-1 [78.7 kB] Get:182 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-9-1 [1450 kB] Get:183 http://deb.debian.org/debian sid/main amd64 r-cran-nlme amd64 3.1.170-1 [2330 kB] Get:184 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-6-1 [4192 kB] Get:185 http://deb.debian.org/debian sid/main amd64 r-cran-mgcv amd64 1.9-4-1 [3608 kB] Get:186 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.5.0-3 [503 kB] Get:187 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.24.0-1 [444 kB] Get:188 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.72.0-1 [2320 kB] Get:189 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.3.0-1 [871 kB] Get:190 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.6.0+dfsg-3 [452 kB] Get:191 http://deb.debian.org/debian sid/main amd64 r-cran-bit64 amd64 4.8.2-1 [585 kB] Get:192 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.3.0-1 [54.1 kB] Get:193 http://deb.debian.org/debian sid/main amd64 r-cran-fastmap amd64 1.2.0-3 [79.8 kB] Get:194 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.1.0-3 [79.6 kB] Get:195 http://deb.debian.org/debian sid/main amd64 r-cran-memoise all 2.0.1-2 [54.3 kB] Get:196 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-3 [21.7 kB] Get:197 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.5-1 [236 kB] Get:198 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.4.6-1 [1236 kB] Get:199 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-9-1 [42.9 kB] Get:200 http://deb.debian.org/debian sid/main amd64 r-bioc-seqinfo all 1.2.0+dfsg-1 [390 kB] Get:201 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.3-2 [164 kB] Get:202 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.80.1+dfsg-1 [13.3 MB] Get:203 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.52.2+dfsg-1 [189 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.74.0-1 [4484 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:206 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.23-1 [1754 kB] Get:207 http://deb.debian.org/debian sid/main amd64 r-cran-xtable all 1:1.8-8-1 [737 kB] Get:208 http://deb.debian.org/debian sid/main amd64 r-bioc-annotate all 1.90.0+dfsg-1 [1861 kB] Get:209 http://deb.debian.org/debian sid/main amd64 r-cran-survival amd64 3.8-9-1 [8191 kB] Get:210 http://deb.debian.org/debian sid/main amd64 r-bioc-genefilter amd64 1.94.0-2+b1 [1240 kB] Get:211 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-3 [152 kB] Get:212 http://deb.debian.org/debian sid/main amd64 r-cran-lambda.r all 1.2.4-3 [119 kB] Get:213 http://deb.debian.org/debian sid/main amd64 r-cran-futile.options all 1.0.1-4 [20.6 kB] Get:214 http://deb.debian.org/debian sid/main amd64 r-cran-futile.logger all 1.4.9-2 [121 kB] Get:215 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.90.0-1 [6220 B] Get:216 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.46.0-1 [971 kB] Get:217 http://deb.debian.org/debian sid/main amd64 r-cran-statmod amd64 1.5.2-1 [307 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-bioc-limma amd64 3.68.4+dfsg-1 [2046 kB] Get:219 http://deb.debian.org/debian sid/main amd64 r-cran-locfit amd64 1.5-9.12-2 [513 kB] Get:220 http://deb.debian.org/debian sid/main amd64 r-bioc-edger amd64 4.10.1+dfsg-1 [1201 kB] Get:221 http://deb.debian.org/debian sid/main amd64 r-bioc-sva amd64 3.60.0+ds-1+b1 [455 kB] Get:222 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges all 1.64.0+dfsg-1 [2087 kB] Get:223 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.12.0+dfsg-1 [822 kB] Get:224 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.12.2+dfsg-1 [1407 kB] Get:225 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray all 0.38.2+dfsg-1 [1999 kB] Get:226 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.42.0+dfsg-1 [1119 kB] Get:227 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.1-0-1 [31.0 kB] Get:228 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.28.0+dfsg-1+b1 [2625 kB] Get:229 http://deb.debian.org/debian sid/main amd64 r-bioc-cigarillo amd64 1.2.1+dfsg-1 [141 kB] Get:230 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.48.0-1 [2132 kB] Get:231 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.22.0+dfsg-1 [213 kB] Get:232 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.19+dfsg-1 [801 kB] Get:233 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.23-1+b1 [101 kB] Get:234 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.17-1 [392 kB] Get:235 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.72.0+ds-1 [5181 kB] Get:236 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.48.0+dfsg-1 [3545 kB] Get:237 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.4-1 [84.2 kB] Get:238 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.8.0+dfsg-1 [1344 kB] Get:239 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.58.1-1 [649 kB] Get:240 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.7.0-8 [246 kB] Get:241 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:242 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.9.3-1+b1 [18.2 kB] Get:243 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Get:244 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.7.0-8 [66.9 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.7.0-8 [46.3 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.7.0-8 [168 kB] Get:247 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.42.2-2 [119 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.4.0-1 [37.1 kB] Get:249 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.6.0-1 [24.7 kB] Get:250 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.78-1 [26.9 kB] Get:251 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.53.4-2 [974 kB] Get:252 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.42.2-2 [24.6 kB] Get:253 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.2.0-2 [43.2 kB] Get:254 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.19.3-2 [208 kB] Get:255 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20260302-1 [142 kB] Get:256 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Get:257 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.11-1 [7148 B] Get:258 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.11-1 [307 kB] Get:259 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.11-1 [93.2 kB] Get:260 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.19.3-2 [1284 kB] Get:261 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.26.4-1 [471 kB] Get:262 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.21.0-2+b1 [49.3 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.13-1 [1546 kB] Get:264 http://deb.debian.org/debian sid/main amd64 libicu76 amd64 76.1-4+b1 [9752 kB] Get:265 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.4 [709 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.15-1 [13.5 MB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-plogr all 0.2.0-4 [15.4 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-2 [54.0 kB] Preconfiguring packages ... Fetched 251 MB in 3s (86.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 35952 files and directories currently installed.) Preparing to unpack .../rpcsvc-proto_1.4.4-1_amd64.deb ... Unpacking rpcsvc-proto (1.4.4-1) over (1.4.3-1) ... Preparing to unpack .../libc-dev-bin_2.43-3_amd64.deb ... Unpacking libc-dev-bin (2.43-3) over (2.41-12+deb13u3) ... Preparing to unpack .../libcrypt1_1%3a4.5.2+20251210-1_amd64.deb ... 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Setting up libngtcp2-16:amd64 (1.24.0-1) ... Setting up libsemanage2:amd64 (3.11-1) ... Setting up mawk (1.3.4.20260302-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libicu76:amd64 (76.1-4+b1) ... Setting up libpaper2:amd64 (2.2.5-0.4) ... Setting up libssh2-1t64:amd64 (1.11.1-5) ... Setting up libtsan2:amd64 (16.2.0-1) ... Setting up libc-dev-bin (2.43-3) ... Setting up gcc-15-base:amd64 (15.3.0-2) ... Setting up openssl (3.6.3-1) ... Setting up libbsd0:amd64 (0.12.2-3) ... Setting up readline-common (8.3-4) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.4) ... Setting up libldap2:amd64 (2.6.14+dfsg-1) ... Setting up liblsan0:amd64 (16.2.0-1) ... Setting up libitm1:amd64 (16.2.0-1) ... Setting up login (1:4.16.0-2+really2.42.2-2) ... Installing new version of config file /etc/pam.d/login ... Setting up libice6:amd64 (2:1.1.1-1+b2) ... Setting up liblapack3:amd64 (3.12.1-8) ... Setting up libgcc-15-dev:amd64 (15.3.0-2) ... Setting up libxrender1:amd64 (1:0.9.12-1+b2) ... Setting up fontconfig-config (2.17.1-5) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up libidn2-0:amd64 (2.3.8-5) ... Setting up libpaper-utils (2.2.5-0.4) ... Setting up libthai0:amd64 (0.1.30-3) ... Setting up ca-certificates (20260601) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt, it does not contain exactly one certificate or CRL 6 added, 35 removed; done. Setting up libglib2.0-0t64:amd64 (2.88.3-2) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.14.3+dfsg-2) ... Setting up libp11-kit0:amd64 (0.26.4-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up ucf (3.0056) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.24.0-1) ... Setting up libreadline8t64:amd64 (8.3-4) ... Setting up passwd (1:4.19.3-2) ... Setting up libc6-dev:amd64 (2.43-3) ... Setting up libharfbuzz0b:amd64 (12.3.2-2+b2) ... Setting up libxss1:amd64 (1:1.2.3-1+b4) ... Setting up libfontconfig1:amd64 (2.17.1-5) ... Setting up libgcc-14-dev:amd64 (14.4.0-1) ... Setting up libstdc++-14-dev:amd64 (14.4.0-1) ... Setting up libsm6:amd64 (2:1.2.6-1+b2) ... Setting up libgnutls30t64:amd64 (3.8.13-1) ... Setting up fontconfig (2.17.1-5) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b5) ... Setting up libtirpc3t64:amd64 (1.3.7+ds-1) ... Setting up libtk8.6:amd64 (8.6.18-1) ... Setting up libpango-1.0-0:amd64 (1.58.0-1) ... Setting up libpsl5t64:amd64 (0.23.2-1) ... Setting up libcairo2:amd64 (1.18.4-3+b1) ... Setting up libstdc++-15-dev:amd64 (15.3.0-2) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.3+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up libboost1.90-dev:amd64 (1.90.0-6) ... Setting up libboost-dev:amd64 (1.90.0.2) ... Setting up libpangoft2-1.0-0:amd64 (1.58.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.58.0-1) ... Setting up libcurl4t64:amd64 (8.21.0-2) ... Setting up r-base-core (4.6.1-4) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/Renviron.site ... Replacing config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.3-2) ... Setting up r-cran-futile.options (1.0.1-4) ... Setting up r-cran-lattice (0.22-9-1) ... Setting up r-cran-nlme (3.1.170-1) ... Setting up r-cran-formatr (1.14-3) ... Setting up r-cran-xml (3.99-0.23-1) ... Setting up r-cran-locfit (1.5-9.12-2) ... Setting up r-cran-statmod (1.5.2-1) ... Setting up r-cran-rjson (0.2.23-1+b1) ... Setting up r-cran-r6 (2.6.1-2) ... Setting up r-bioc-genomeinfodbdata (1.2.15-1) ... Setting up r-cran-bh (1.90.0-1) ... Setting up r-cran-curl (7.1.0+dfsg-2) ... Setting up r-cran-rlang (1.3.0-1) ... Setting up r-cran-matrixstats (1.5.0-3) ... Setting up r-cran-sys (3.4.3-3) ... Setting up r-cran-plogr (0.2.0-4) ... Setting up r-cran-mime (0.13-2) ... Setting up r-cran-generics (0.1.4-1) ... Setting up r-cran-yaml (2.3.12-2) ... Setting up r-cran-lambda.r (1.2.4-3) ... Setting up r-cran-dbi (1.3.0-1) ... Setting up r-cran-glue (1.8.1-2) ... Setting up r-cran-bit (4.6.0+dfsg-3) ... Setting up r-cran-xtable (1:1.8-8-1) ... Setting up r-cran-cli (3.6.6-1) ... Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... Setting up r-cran-bitops (1.1-0-1) ... Setting up r-cran-bit64 (4.8.2-1) ... Setting up r-cran-askpass (1.2.1-3) ... Setting up r-cran-fastmap (1.2.0-3) ... Setting up r-cran-png (0.1-9-1) ... Setting up r-cran-jsonlite (2.0.0+dfsg-2) ... Setting up r-cran-pkgconfig (2.0.3-3) ... Setting up r-cran-cpp11 (0.5.5-1) ... Setting up r-cran-rcolorbrewer (1.1-3-2) ... Setting up r-cran-futile.logger (1.4.9-2) ... Setting up r-cran-matrix (1.7-6-1) ... Setting up r-cran-mgcv (1.9-4-1) ... Setting up r-cran-cachem (1.1.0-3) ... Setting up r-cran-rcurl (1.98-1.19+dfsg-1) ... Setting up r-cran-vctrs (0.7.3-2) ... Setting up r-cran-openssl (2.4.2+dfsg-1) ... Setting up r-bioc-biocgenerics (0.58.1-1) ... Setting up r-bioc-biocparallel (1.46.0-1) ... Setting up r-bioc-matrixgenerics (1.24.0-1) ... Setting up r-bioc-rhtslib (3.8.0+dfsg-1) ... Setting up r-cran-survival (3.8-9-1) ... Setting up r-bioc-biobase (2.72.0-1) ... Setting up r-cran-httr (1.4.8+dfsg-1) ... Setting up r-bioc-s4vectors (0.50.1+dfsg-1) ... Setting up r-cran-memoise (2.0.1-2) ... Setting up r-bioc-limma (3.68.4+dfsg-1) ... Setting up r-cran-blob (1.3.0-1) ... Setting up r-bioc-iranges (2.46.0-1) ... Setting up r-cran-rsqlite (2.4.6-1) ... Setting up r-cran-restfulr (0.0.17-1) ... Setting up r-bioc-s4arrays (1.12.0+dfsg-1) ... Setting up r-bioc-ucsc.utils (1.8.0+dfsg-1) ... Setting up r-bioc-edger (4.10.1+dfsg-1) ... Setting up r-bioc-biocio (1.22.0+dfsg-1) ... Setting up r-bioc-seqinfo (1.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.48.0+dfsg-1) ... Setting up r-bioc-xvector (0.52.0-1) ... Setting up r-bioc-sparsearray (1.12.2+dfsg-1) ... Setting up r-bioc-genomicranges (1.64.0+dfsg-1) ... Setting up r-bioc-biostrings (2.80.1+dfsg-1) ... Setting up r-bioc-rsamtools (2.28.0+dfsg-1+b1) ... Setting up r-bioc-cigarillo (1.2.1+dfsg-1) ... Setting up r-bioc-delayedarray (0.38.2+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.42.0+dfsg-1) ... Setting up r-bioc-keggrest (1.52.2+dfsg-1) ... Setting up r-bioc-annotationdbi (1.74.0-1) ... Setting up r-bioc-annotate (1.90.0+dfsg-1) ... Setting up r-bioc-genefilter (1.94.0-2+b1) ... Setting up r-bioc-genomicalignments (1.48.0-1) ... Setting up r-bioc-rtracklayer (1.72.0+ds-1) ... Setting up r-bioc-sva (3.60.0+ds-1+b1) ... Processing triggers for libc-bin (2.43-3) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for ca-certificates (20260601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-yf', 'dist-upgrade'] 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m9.2s DUMP: a1365537c8748e6813af86e86c5c09c2 - 1m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-ballgown'] 1m9.4s DUMP: Package: r-bioc-ballgown Version: 2.43.0+dfsg-1 Installed-Size: 4503 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-RELEASE, r-bioc-genomicranges (>= 1.17.25), r-bioc-iranges (>= 1.99.22), r-bioc-s4vectors (>= 0.9.39), r-cran-rcolorbrewer, r-bioc-sva, r-bioc-limma, r-bioc-rtracklayer (>= 1.29.25), r-bioc-biobase (>= 2.25.0), r-bioc-seqinfo, r-pkg-team-core-architecture Suggests: r-cran-testthat, r-cran-knitr, r-cran-markdown Description-en: Flexible, isoform-level differential expression analysis Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. Description-md5: f4ae5d7c8c9bcfa4c48b5e78d093a9f0 Homepage: https://bioconductor.org/packages/ballgown/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-ballgown/r-bioc-ballgown_2.43.0+dfsg-1_all.deb Size: 2922180 MD5sum: a09e750608e51ab718094f0ac2aa41be SHA256: 2aa600fe90cc7fce22c727201eff0dcd9d24c6920e3ae3be41a5da067855d9aa 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-ballgown'] 1m9.4s INFO: apt-cache knows about the following packages: r-bioc-ballgown 1m9.4s INFO: Running scripts pre_install 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_database-server'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_database-server'] 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_exceptions'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_exceptions'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_extras'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_extras'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy'] 1m9.5s 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: 1m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy'] 1m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy', 'r-bioc-ballgown'] 1m9.6s DUMP: r-bioc-ballgown: Installed: (none) Candidate: 2.43.0+dfsg-1 Version table: 2.43.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 1m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-cache', 'policy', 'r-bioc-ballgown'] 1m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-y', 'install', 'r-bioc-ballgown'] 1m10.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-ballgown : Depends: r-api-bioc-RELEASE but it is not installable E: Unable to satisfy dependencies. Reached two conflicting assignments: 1. r-bioc-ballgown:amd64=2.43.0+dfsg-1 is selected for install 2. r-bioc-ballgown:amd64 Depends r-api-bioc-RELEASE but none of the choices are installable: [no choices] 1m10.2s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmp9604zi98', 'apt-get', '-y', 'install', 'r-bioc-ballgown'] Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-ballgown : Depends: r-api-bioc-RELEASE but it is not installable E: Unable to satisfy dependencies. Reached two conflicting assignments: 1. r-bioc-ballgown:amd64=2.43.0+dfsg-1 is selected for install 2. r-bioc-ballgown:amd64 Depends r-api-bioc-RELEASE but none of the choices are installable: [no choices] 1m11.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/shm'] 1m11.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/shm'] 1m11.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/console'] 1m11.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/console'] 1m11.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/ptmx'] 1m11.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/ptmx'] 1m11.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts'] 1m11.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/dev/pts'] 1m11.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/proc'] 1m11.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9604zi98/proc'] 1m11.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 1m12.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9604zi98'] 1m12.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp9604zi98 1m12.2s ERROR: piuparts run ends. ret=1 End: 2026-08-12 05:20:44 GMT