Start: 2024-12-18 22:33:59 GMT [sid] Package: r-bioc-bsseq Version: 1.40.0+dfsg-1 Installed-Size: 3496 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-genomicranges (>= 1.56.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomeinfodb (>= 1.40.1), r-cran-scales, r-bioc-biobase (>= 2.64.0), r-cran-locfit, r-cran-gtools, r-cran-data.table (>= 1.11.8), r-bioc-s4vectors (>= 0.42.1), r-cran-r.utils (>= 2.0.0), r-bioc-delayedmatrixstats (>= 1.26.0), r-cran-permute, r-bioc-limma (>= 3.60.3), r-bioc-delayedarray (>= 0.30.1), r-cran-rcpp, r-bioc-biocparallel (>= 1.38.0), r-bioc-bsgenome (>= 1.72.0), r-bioc-biostrings (>= 2.72.1), r-bioc-hdf5array (>= 1.32.0), r-bioc-rhdf5 (>= 2.48.0), r-bioc-beachmat (>= 2.20.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Suggests: r-cran-testthat, r-bioc-biocstyle (>= 2.32.1), r-cran-rmarkdown, r-cran-knitr, r-cran-matrix, r-cran-doparallel, r-bioc-rtracklayer (>= 1.64.0), r-cran-batchtools Description: Bioconductor analyze, manage and store bisulfite sequencing data Homepage: https://bioconductor.org/packages/bsseq/ Description-md5: 180b48f012fc46f936094bed692669d0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-bsseq/r-bioc-bsseq_1.40.0+dfsg-1_amd64.deb Size: 2965072 MD5sum: 6dbd56fe0f6b86495c03717db778e173 SHA256: d06114c7dd4f0ca385f30e7cb1f04aef7749d244612d24c47e15ddbeac2b3e03 [experimental] Package: r-bioc-bsseq Version: 1.42.0+dfsg-1 Installed-Size: 3596 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-biocgenerics, r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.19.5), r-bioc-iranges (>= 2.23.9), r-bioc-genomeinfodb, r-cran-scales, r-bioc-biobase, r-cran-locfit, r-cran-gtools, r-cran-data.table (>= 1.11.8), r-bioc-s4vectors (>= 0.27.12), r-cran-r.utils (>= 2.0.0), r-bioc-delayedmatrixstats (>= 1.5.2), r-cran-permute, r-bioc-limma, r-bioc-delayedarray (>= 0.15.16), r-cran-rcpp, r-bioc-biocparallel, r-bioc-bsgenome, r-bioc-biostrings, r-bioc-hdf5array (>= 1.19.11), r-bioc-rhdf5, r-bioc-beachmat, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Suggests: r-cran-testthat, r-bioc-biocstyle, r-cran-rmarkdown, r-cran-knitr, r-cran-matrix, r-cran-doparallel, r-bioc-rtracklayer, r-bioc-beachmat (>= 1.5.2), r-cran-batchtools Description: Bioconductor analyze, manage and store bisulfite sequencing data Homepage: https://bioconductor.org/packages/bsseq/ Description-md5: 180b48f012fc46f936094bed692669d0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-bsseq/r-bioc-bsseq_1.42.0+dfsg-1_amd64.deb Size: 3056380 MD5sum: f8c3b8efb4a662c08ac257665732d2a5 SHA256: abb2f0878ac5225847dbc7dcd08758f8dcdca881ef74231e8feef75cb43336dd Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt r-bioc-bsseq=1.42.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt r-bioc-bsseq=1.42.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpmyph3wyc 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmyph3wyc 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/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/tmpmyph3wyc/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/tmpmyph3wyc/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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/tmpmyph3wyc/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', 'update'] 0m2.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7353 kB] Fetched 17.6 MB in 2s (11.6 MB/s) Reading package lists... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', 'update'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s DUMP: 212d2619526b74db74ceed03c745b3df - 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.8s INFO: Running scripts post_setup 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_minimize'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_setup_zz_backports'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DUMP: install ok installed apt apt 2.9.17 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-12 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2~rc1-2 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-11 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.17 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-12 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2~rc1-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.274 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2~rc1-2 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-11 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.51-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-12 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-12 install ok installed libss2:amd64 libss2 1.47.2~rc1-2 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-11 install ok installed libsystemd0:amd64 libsystemd0 257-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257-2 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-12 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-12 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2~rc1-2 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-12 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-12 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-bsseq'] 0m3.7s DUMP: Package: r-bioc-bsseq Version: 1.40.0+dfsg-1 Installed-Size: 3496 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-genomicranges (>= 1.56.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomeinfodb (>= 1.40.1), r-cran-scales, r-bioc-biobase (>= 2.64.0), r-cran-locfit, r-cran-gtools, r-cran-data.table (>= 1.11.8), r-bioc-s4vectors (>= 0.42.1), r-cran-r.utils (>= 2.0.0), r-bioc-delayedmatrixstats (>= 1.26.0), r-cran-permute, r-bioc-limma (>= 3.60.3), r-bioc-delayedarray (>= 0.30.1), r-cran-rcpp, r-bioc-biocparallel (>= 1.38.0), r-bioc-bsgenome (>= 1.72.0), r-bioc-biostrings (>= 2.72.1), r-bioc-hdf5array (>= 1.32.0), r-bioc-rhdf5 (>= 2.48.0), r-bioc-beachmat (>= 2.20.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Suggests: r-cran-testthat, r-bioc-biocstyle (>= 2.32.1), r-cran-rmarkdown, r-cran-knitr, r-cran-matrix, r-cran-doparallel, r-bioc-rtracklayer (>= 1.64.0), r-cran-batchtools Description-en: Bioconductor analyze, manage and store bisulfite sequencing data A collection of tools for analyzing and visualizing bisulfite sequencing data. Description-md5: 180b48f012fc46f936094bed692669d0 Homepage: https://bioconductor.org/packages/bsseq/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-bsseq/r-bioc-bsseq_1.40.0+dfsg-1_amd64.deb Size: 2965072 MD5sum: 6dbd56fe0f6b86495c03717db778e173 SHA256: d06114c7dd4f0ca385f30e7cb1f04aef7749d244612d24c47e15ddbeac2b3e03 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-bsseq'] 0m3.7s INFO: apt-cache knows about the following packages: r-bioc-bsseq 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy'] 0m3.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy', 'r-bioc-bsseq'] 0m3.8s DUMP: r-bioc-bsseq: Installed: (none) Candidate: 1.40.0+dfsg-1 Version table: 1.40.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy', 'r-bioc-bsseq'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-y', 'install', 'r-bioc-bsseq'] 0m23.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates comerr-dev fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hdf5-helpers krb5-multidev libaec-dev libaec0 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.83-dev libbrotli-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4-openssl-dev libcurl4t64 libdatrie1 libdeflate0 libevent-2.1-7t64 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssrpc4t64 libharfbuzz0b libhdf5-103-1t64 libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhwasan0 libice6 libicu72 libidn2-dev libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 liblapack3 libldap-2.5-0 libldap-dev liblerc4 liblsan0 libncursesw6 libnghttp2-14 libnghttp2-dev libp11-kit-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpkgconf3 libpng16-16t64 libproc2-0 libpsl-dev libpsl5t64 libquadmath0 libreadline8t64 librtmp-dev librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsnappy1v5 libssh2-1-dev libssh2-1t64 libssl-dev libstdc++-14-dev libsz2 libtasn1-6-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev littler nettle-dev openssl perl perl-modules-5.40 pkgconf pkgconf-bin procps r-base-core r-bioc-beachmat r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-delayedmatrixstats r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-hdf5array r-bioc-iranges r-bioc-limma r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-sparsematrixstats r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bh r-cran-bitops r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-farver r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-gtools r-cran-httr r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-mime r-cran-munsell r-cran-openssl r-cran-permute r-cran-pkgkitten r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-scales r-cran-snow r-cran-statmod r-cran-sys r-cran-viridislite r-cran-xml r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: doc-base krb5-doc 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 dpkg-dev libcurl4-doc libidn-dev gdbm-l10n low-memory-monitor gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user libhdf5-doc libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-testthat r-bioc-biocstyle r-cran-knitr r-cran-rmarkdown r-cran-rcmdcheck r-bioc-all r-cran-runit r-bioc-golubesets r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-bbmisc r-cran-doparallel r-bioc-variantannotation r-bioc-shortread r-cran-batchtools r-bioc-pwalign r-bioc-genomicfeatures r-cran-biocmanager r-bioc-genefilter r-cran-lobstr r-cran-microbenchmark r-cran-profmem r-bioc-edger r-bioc-txdbmaker r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-keggrest r-cran-digest r-bioc-experimenthub r-bioc-singlecellexperiment r-cran-biasedurn r-cran-ellipse r-cran-gplots r-cran-mass r-bioc-go.db r-bioc-org.hs.eg.db r-cran-bit64 r-cran-bench r-cran-dplyr r-cran-ggplot2 r-cran-mockery r-cran-tinytest r-bioc-graph r-cran-dbi r-cran-rmariadb r-cran-rstudioapi r-cran-getopt r-cran-interp r-cran-gam r-cran-vegan r-cran-bookdown r-cran-sessioninfo r-cran-inline r-cran-rmpi r-cran-rlecuyer readline-doc Recommended packages: manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libtasn1-doc netbase psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-callr r-cran-covr r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-tibble r-cran-whoami r-cran-withr r-cran-kernsmooth r-cran-mass r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-ggplot2 r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-progress r-cran-vctrs r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-bit64 r-cran-bit r-cran-xts r-cran-zoo r-cran-markdown r-cran-testit r-cran-survival r-cran-dbi r-cran-magrittr r-cran-rsqlite r-cran-waldo r-cran-readr r-cran-xml2 r-cran-r.rsp r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-microbenchmark r-cran-r.devices r-cran-sodium r-cran-runit r-cran-fs r-cran-pillar r-cran-usethis r-cran-dichromat r-cran-hms r-cran-stringi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates comerr-dev fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono hdf5-helpers krb5-multidev libaec-dev libaec0 libasan8 libatomic1 libblas3 libblosc1 libboost-dev libboost1.83-dev libbrotli-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4-openssl-dev libcurl4t64 libdatrie1 libdeflate0 libevent-2.1-7t64 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssapi-krb5-2 libgssrpc4t64 libharfbuzz0b libhdf5-103-1t64 libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhwasan0 libice6 libicu72 libidn2-dev libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 liblapack3 libldap-2.5-0 libldap-dev liblerc4 liblsan0 libncursesw6 libnghttp2-14 libnghttp2-dev libp11-kit-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpkgconf3 libpng16-16t64 libproc2-0 libpsl-dev libpsl5t64 libquadmath0 libreadline8t64 librtmp-dev librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libsnappy1v5 libssh2-1-dev libssh2-1t64 libssl-dev libstdc++-14-dev libsz2 libtasn1-6-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev littler nettle-dev openssl perl perl-modules-5.40 pkgconf pkgconf-bin procps r-base-core r-bioc-beachmat r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biostrings r-bioc-bsgenome r-bioc-bsseq r-bioc-delayedarray r-bioc-delayedmatrixstats r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-hdf5array r-bioc-iranges r-bioc-limma r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-sparsematrixstats r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bh r-cran-bitops r-cran-cli r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-farver r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-gtools r-cran-httr r-cran-jsonlite r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-mime r-cran-munsell r-cran-openssl r-cran-permute r-cran-pkgkitten r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-scales r-cran-snow r-cran-statmod r-cran-sys r-cran-viridislite r-cran-xml r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 232 newly installed, 0 to remove and 0 not upgraded. Need to get 227 MB of archives. After this operation, 706 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:4 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB] Get:5 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:6 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:7 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:8 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:12 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-8 [267 kB] Get:13 http://deb.debian.org/debian sid/main amd64 ucf all 3.0045 [45.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.40-4 [52.0 kB] Get:15 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.5-1 [2474 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:17 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.40-4 [1954 kB] Get:19 http://deb.debian.org/debian sid/main amd64 comerr-dev amd64 2.1-1.47.2~rc1-2 [55.4 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:24 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:25 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:26 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:28 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:29 http://deb.debian.org/debian sid/main amd64 hdf5-helpers amd64 1.14.5+repack-1 [26.3 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:33 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get:39 http://deb.debian.org/debian sid/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get:42 http://deb.debian.org/debian sid/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-11 [2728 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-11 [9284 B] Get:45 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libblosc1 amd64 1.21.5+ds-1+b2 [49.5 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-11 [137 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-11 [26.0 kB] Get:50 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-11 [1205 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-11 [2461 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-11 [1075 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-11 [1489 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-11 [146 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-11 [2673 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-11 [2373 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get:58 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:59 http://deb.debian.org/debian sid/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:76 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:83 http://deb.debian.org/debian sid/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:84 http://deb.debian.org/debian sid/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get:95 http://deb.debian.org/debian sid/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get:97 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:98 http://deb.debian.org/debian sid/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libcurl4-openssl-dev amd64 8.11.1-1 [464 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5+b1 [1254 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libhdf5-310 amd64 1.14.5+repack-1 [1340 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-1 [133 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-1 [112 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-1 [69.0 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-1 [43.6 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-1 [24.1 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libhdf5-dev amd64 1.14.5+repack-1 [3165 kB] Get:121 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:125 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:126 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:134 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:147 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB] Get:148 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:149 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:150 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:151 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get:152 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-2 [16.0 kB] Get:153 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:154 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:155 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:156 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:157 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:158 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:159 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:160 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB] Get:161 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:162 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:163 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:164 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:165 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:166 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:167 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:168 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:169 http://deb.debian.org/debian sid/main amd64 r-bioc-beachmat amd64 2.20.0+ds-1 [1386 kB] Get:170 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:171 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:172 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:173 http://deb.debian.org/debian sid/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:174 http://deb.debian.org/debian sid/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:178 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:179 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:180 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:181 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:182 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:183 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:184 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:185 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:186 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:187 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:188 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:189 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:190 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:191 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:192 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:193 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.2+dfsg-1 [1843 kB] Get:194 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:195 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.0-8-1 [30.7 kB] Get:196 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:197 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:198 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:199 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:200 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB] Get:201 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB] Get:202 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:203 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:205 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.72.0-1 [6812 kB] Get:206 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:207 http://deb.debian.org/debian sid/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:208 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:209 http://deb.debian.org/debian sid/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:210 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:211 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:212 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:213 http://deb.debian.org/debian sid/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:214 http://deb.debian.org/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:215 http://deb.debian.org/debian sid/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:216 http://deb.debian.org/debian sid/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:217 http://deb.debian.org/debian sid/main amd64 r-cran-locfit amd64 1.5-9.10-1 [515 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-cran-gtools amd64 3.9.5-1 [362 kB] Get:219 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:220 http://deb.debian.org/debian sid/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get:221 http://deb.debian.org/debian sid/main amd64 r-cran-r.oo all 1.26.0-1 [961 kB] Get:222 http://deb.debian.org/debian sid/main amd64 r-cran-r.utils all 2.12.3-1 [1396 kB] Get:223 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsematrixstats amd64 1.16.0+dfsg-1 [922 kB] Get:224 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedmatrixstats all 1.26.0+ds-1 [487 kB] Get:225 http://deb.debian.org/debian sid/main amd64 r-cran-permute all 0.9-7-1 [225 kB] Get:226 http://deb.debian.org/debian sid/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:227 http://deb.debian.org/debian sid/main amd64 r-bioc-limma amd64 3.60.6+dfsg-1 [2006 kB] Get:228 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5lib amd64 1.26.0+dfsg-1+b1 [104 kB] Get:229 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5filters amd64 1.16.0+dfsg-1 [139 kB] Get:230 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5 amd64 2.48.0+dfsg-3 [857 kB] Get:231 http://deb.debian.org/debian sid/main amd64 r-bioc-hdf5array amd64 1.32.1-1+b1 [8773 kB] Get:232 http://deb.debian.org/debian sid/main amd64 r-bioc-bsseq amd64 1.40.0+dfsg-1 [2965 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 227 MB in 4s (57.1 MB/s) Selecting previously unselected package libncursesw6: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 ... 5135 files and directories currently installed.) Preparing to unpack .../000-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_amd64.deb ... 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Preparing to unpack .../133-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../134-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../135-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../141-libxft2_2.3.6-1+b3_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../142-libxss1_1%3a1.2.3-1+b2_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../143-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../144-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-permute (0.9-7-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up littler (0.3.20-2) ... Setting up r-bioc-matrixgenerics (1.16.0-2) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-abind (1.4-8-1) ... Setting up r-cran-yaml (2.3.10-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-gtools (3.9.5-1) ... Setting up r-cran-data.table (1.16.2+dfsg-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bitops (1.0-8-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-cran-r.methodss3 (1.8.2-1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up r-cran-jsonlite (1.8.9+dfsg-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up libcurl4-openssl-dev:amd64 (8.11.1-1) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up libhdf5-dev (1.14.5+repack-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up r-bioc-limma (3.60.6+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-bioc-sparsematrixstats (1.16.0+dfsg-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-bioc-rhdf5lib (1.26.0+dfsg-1+b1) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up r-cran-r.oo (1.26.0-1) ... Setting up r-bioc-rhdf5filters (1.16.0+dfsg-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-r.utils (2.12.3-1) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-bioc-rhdf5 (2.48.0+dfsg-3) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up r-bioc-hdf5array (1.32.1-1+b1) ... Setting up r-bioc-genomicranges (1.56.2+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-bioc-delayedmatrixstats (1.26.0+ds-1) ... Setting up r-bioc-beachmat (2.20.0+ds-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-bioc-bsgenome (1.72.0-1) ... Setting up r-bioc-bsseq (1.40.0+dfsg-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-y', 'install', 'r-bioc-bsseq'] 0m23.5s INFO: Running scripts post_install 0m23.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/post_install_exceptions'] 0m23.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m24.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m24.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpmyph3wyc to experimental 0m24.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m24.7s INFO: Running scripts pre_distupgrade 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_exceptions'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', 'update'] 0m25.6s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [437 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [274 kB] Fetched 812 kB in 0s (2226 kB/s) Reading package lists... 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', 'update'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-yf', 'dist-upgrade'] 0m25.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-yf', 'dist-upgrade'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m26.1s DUMP: ca19809fe8b1f1d7c50535c77ec70be9 - 0m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-bsseq'] 0m26.2s DUMP: Package: r-bioc-bsseq Version: 1.40.0+dfsg-1 Installed-Size: 3496 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biocgenerics (>= 0.50.0), r-bioc-genomicranges (>= 1.56.1), r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-iranges (>= 2.38.1), r-bioc-genomeinfodb (>= 1.40.1), r-cran-scales, r-bioc-biobase (>= 2.64.0), r-cran-locfit, r-cran-gtools, r-cran-data.table (>= 1.11.8), r-bioc-s4vectors (>= 0.42.1), r-cran-r.utils (>= 2.0.0), r-bioc-delayedmatrixstats (>= 1.26.0), r-cran-permute, r-bioc-limma (>= 3.60.3), r-bioc-delayedarray (>= 0.30.1), r-cran-rcpp, r-bioc-biocparallel (>= 1.38.0), r-bioc-bsgenome (>= 1.72.0), r-bioc-biostrings (>= 2.72.1), r-bioc-hdf5array (>= 1.32.0), r-bioc-rhdf5 (>= 2.48.0), r-bioc-beachmat (>= 2.20.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1) Suggests: r-cran-testthat, r-bioc-biocstyle (>= 2.32.1), r-cran-rmarkdown, r-cran-knitr, r-cran-matrix, r-cran-doparallel, r-bioc-rtracklayer (>= 1.64.0), r-cran-batchtools Description-en: Bioconductor analyze, manage and store bisulfite sequencing data A collection of tools for analyzing and visualizing bisulfite sequencing data. Description-md5: 180b48f012fc46f936094bed692669d0 Homepage: https://bioconductor.org/packages/bsseq/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-bsseq/r-bioc-bsseq_1.40.0+dfsg-1_amd64.deb Size: 2965072 MD5sum: 6dbd56fe0f6b86495c03717db778e173 SHA256: d06114c7dd4f0ca385f30e7cb1f04aef7749d244612d24c47e15ddbeac2b3e03 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-bsseq'] 0m26.2s INFO: apt-cache knows about the following packages: r-bioc-bsseq 0m26.2s INFO: Running scripts pre_install 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_database-server'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_database-server'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_exceptions'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_exceptions'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_extras'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_extras'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy'] 0m26.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy', 'r-bioc-bsseq'] 0m26.3s DUMP: r-bioc-bsseq: Installed: 1.40.0+dfsg-1 Candidate: 1.40.0+dfsg-1 Version table: 1.42.0+dfsg-1 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 1.40.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-cache', 'policy', 'r-bioc-bsseq'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-y', '-t', 'experimental', 'install', 'r-bioc-bsseq'] 0m26.6s DUMP: Reading package lists... Building dependency tree... Reading state information... 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-beachmat : Depends: r-api-bioc-3.19 E: Unable to correct problems, you have held broken packages. 0m26.6s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc', 'apt-get', '-y', '-t', 'experimental', 'install', 'r-bioc-bsseq'] Reading package lists... Building dependency tree... Reading state information... 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-beachmat : Depends: r-api-bioc-3.19 E: Unable to correct problems, you have held broken packages. 0m27.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/shm'] 0m27.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/shm'] 0m27.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/console'] 0m27.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/console'] 0m27.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/ptmx'] 0m27.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/ptmx'] 0m27.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/pts'] 0m27.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/dev/pts'] 0m27.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/proc'] 0m27.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc/proc'] 0m27.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m28.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmyph3wyc'] 0m28.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmyph3wyc 0m28.2s ERROR: piuparts run ends. ret=1 End: 2024-12-18 22:34:27 GMT