Start: 2024-03-17 06:53:36 GMT [stable] Package: r-bioc-variantannotation Version: 1.36.0-1 Installed-Size: 4819 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-biocgenerics (>= 0.15.3), r-bioc-matrixgenerics, r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.19.5), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-xvector (>= 0.29.2), r-bioc-biostrings (>= 2.57.2), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib, libc6 (>= 2.15), libcurl4 (>= 7.18.0) Recommends: r-cran-runit, r-bioc-snpstats Suggests: r-bioc-annotationhub, r-cran-ggplot2, r-bioc-biocstyle Description: BioConductor annotation of genetic variants Homepage: https://bioconductor.org/packages/VariantAnnotation/ Description-md5: 17670e83de551a30abddcb85706e9bf5 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.36.0-1_amd64.deb Size: 3501412 MD5sum: 664411ff79a1ebfe84e2aa5af411cea3 SHA256: ff6a7938673a963f171dc6caef233c5475d7fddf26abcd62bd4cffe7615bff04 [sid] Package: r-bioc-variantannotation Source: r-bioc-variantannotation (1.48.1-1) Version: 1.48.1-1+b1 Installed-Size: 6117 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-biocgenerics (>= 0.37.0), r-bioc-matrixgenerics, r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.19.5), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-xvector (>= 0.29.2), r-bioc-biostrings (>= 2.57.2), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib (>= 1.99.3), libbz2-1.0, libc6 (>= 2.34), libcurl4t64 (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.2.3.3) Suggests: r-cran-runit, r-bioc-annotationhub, r-bioc-snpstats, r-cran-ggplot2, r-bioc-biocstyle, r-cran-knitr Description: BioConductor annotation of genetic variants Homepage: https://bioconductor.org/packages/VariantAnnotation/ Description-md5: 17670e83de551a30abddcb85706e9bf5 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.48.1-1+b1_amd64.deb Size: 3500564 MD5sum: 6f6d6fe3baa9a36a47f29706a786d521 SHA256: 8e3f16105e3c4d919b8327da51d9694a888739b5fbfeafda8acf2dab7e37ea96 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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt r-bioc-variantannotation=1.48.1-1+b1 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 1.4.1~202403150926~1.4-1-g8afb49d8 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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt r-bioc-variantannotation=1.48.1-1+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5icx2hzm 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5icx2hzm 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5icx2hzm/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'update'] 0m1.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.usr-is-merged' '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m3.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-variantannotation'] 0m4.5s DUMP: Package: r-bioc-variantannotation Version: 1.36.0-1 Installed-Size: 4819 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.0.3-1), r-api-4.0, r-api-bioc-3.12, r-bioc-biocgenerics (>= 0.15.3), r-bioc-matrixgenerics, r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.19.5), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-xvector (>= 0.29.2), r-bioc-biostrings (>= 2.57.2), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib, libc6 (>= 2.15), libcurl4 (>= 7.18.0) Recommends: r-cran-runit, r-bioc-snpstats Suggests: r-bioc-annotationhub, r-cran-ggplot2, r-bioc-biocstyle Description-en: BioConductor annotation of genetic variants This BioConductor package provides R functions to annotate variants, compute amino acid coding changess and to predict coding outcomes. Description-md5: 17670e83de551a30abddcb85706e9bf5 Homepage: https://bioconductor.org/packages/VariantAnnotation/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.36.0-1_amd64.deb Size: 3501412 MD5sum: 664411ff79a1ebfe84e2aa5af411cea3 SHA256: ff6a7938673a963f171dc6caef233c5475d7fddf26abcd62bd4cffe7615bff04 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-variantannotation'] 0m4.5s INFO: apt-cache knows about the following packages: r-bioc-variantannotation 0m4.5s INFO: Running scripts pre_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 0m4.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 0m4.7s DUMP: r-bioc-variantannotation: Installed: (none) Candidate: 1.36.0-1 Version table: 1.36.0-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation'] 1m27.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo libjs-jquery liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc manpages-dev libstdc++-10-doc tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-org.hs.eg.db r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-rmarkdown r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-bbmisc r-bioc-shortread r-cran-codetools r-cran-data.table r-cran-testthat r-cran-biocmanager r-cran-runit r-bioc-hdf5array r-bioc-genefilter r-bioc-delayedmatrixstats r-bioc-edger r-bioc-ensembldb r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-limma r-bioc-rhdf5 r-cran-ggplot2 r-cran-covr r-cran-roxygen2 r-cran-callr r-cran-htmlwidgets r-cran-ps r-cran-rstudioapi r-cran-prettycode r-cran-rmysql r-cran-bench r-cran-broom r-cran-rpostgresql r-cran-unitizer r-cran-shiny r-cran-r.utils r-cran-forcats r-cran-lubridate r-cran-httpuv r-cran-jpeg r-cran-png r-cran-readr r-cran-plyr r-cran-sf r-cran-getopt r-cran-base64enc r-cran-scales r-cran-inline r-cran-gh r-cran-rvest r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-evaluate r-cran-formattable r-cran-htmltools r-cran-tidyr r-cran-zeallot readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-bioc-go.db r-cran-runit r-cran-testthat r-cran-batchjobs r-cran-doparallel r-cran-batchtools r-cran-rmpi r-bioc-biovizbase r-bioc-shortread r-bioc-annotate r-bioc-snpstats r-cran-mockery r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-data.table r-cran-mass r-cran-testit r-cran-codetools r-cran-survival r-cran-pkgload r-cran-sp r-cran-sodium r-cran-lubridate r-cran-rmarkdown r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockr r-cran-waldo 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 libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo libjs-jquery liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 175 newly installed, 0 to remove and 0 not upgraded. Need to get 178 MB of archives. After this operation, 506 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libasan6 amd64 10.2.1-6 [2065 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libatomic1 amd64 10.2.1-6 [9008 B] Get:17 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libitm1 amd64 10.2.1-6 [25.8 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 liblsan0 amd64 10.2.1-6 [828 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libtsan0 amd64 10.2.1-6 [2000 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libubsan1 amd64 10.2.1-6 [777 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libgcc-10-dev amd64 10.2.1-6 [2328 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libc-dev-bin amd64 2.31-13+deb11u8 [276 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 linux-libc-dev amd64 5.10.209-2 [1698 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libtirpc-dev amd64 1.3.1-1+deb11u1 [191 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libc6-dev amd64 2.31-13+deb11u8 [2361 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] 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libxcb-shm0 amd64 1.14-3 [101 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u11 [347 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u1 [1374 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:89 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 node-html5shiv all 3.7.3+dfsg-3 [12.9 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biobase amd64 2.50.0-1 [2229 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 r-bioc-s4vectors amd64 0.28.1-1 [2027 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 r-bioc-iranges amd64 2.24.1-1 [2202 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbi all 1.1.1-1 [619 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit amd64 4.0.4+dfsg-1 [422 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 r-cran-blob all 1.2.1-2 [49.1 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 r-cran-fastmap amd64 1.1.0-1 [64.7 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 r-cran-cachem amd64 1.0.3-1 [61.4 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 r-cran-memoise all 2.0.0-1 [52.9 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 r-cran-bh all 1.74.0-1 [5196 B] Get:112 http://deb.debian.org/debian bullseye/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 r-cran-rsqlite amd64 2.2.3-1 [1035 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 r-bioc-annotationdbi all 1.52.0-1 [4707 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 r-cran-generics all 0.1.0-1 [73.5 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 r-cran-purrr amd64 0.3.4-1+b1 [398 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyselect amd64 1.1.0+dfsg-1 [192 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 r-cran-dplyr amd64 1.0.4-1 [1143 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 r-cran-dbplyr all 2.1.0-1 [802 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 r-cran-curl amd64 4.3+dfsg-1+b1 [151 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 r-cran-mime amd64 0.9-1+b1 [35.5 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 r-cran-sys amd64 3.4-1 [42.9 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 r-cran-openssl amd64 1.4.3+dfsg-2 [376 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 r-cran-httr all 1.4.2-1 [478 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocfilecache all 1.14.0+dfsg-1 [289 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 r-cran-formatr all 1.7-2 [151 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 r-cran-snow all 1:0.4.3-2 [109 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocparallel amd64 1.24.1-1 [1143 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml amd64 3.99-0.5-1 [1722 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 r-cran-hms all 1.0.0-1 [102 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.5.3-1 [729 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringr all 1.4.0-2 [199 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 r-cran-xml2 amd64 1.3.2-1+b1 [270 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biomart all 2.46.2+dfsg-1 [414 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get:156 http://deb.debian.org/debian bullseye/main amd64 r-bioc-xvector amd64 0.30.0-1 [620 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biostrings amd64 2.58.0-1 [14.2 MB] Get:158 http://deb.debian.org/debian bullseye/main amd64 r-cran-bitops amd64 1.0-6-5 [23.6 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcurl amd64 1.98-1.2-1+b1 [787 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get:161 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicranges amd64 1.42.0+dfsg-1 [1856 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhtslib amd64 1.22.0+dfsg-1 [1024 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rsamtools amd64 2.6.0-1 [3659 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrixstats amd64 0.58.0-3 [664 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 r-bioc-delayedarray amd64 0.16.1+dfsg-1 [1798 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicalignments amd64 1.26.0-1 [2196 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rtracklayer amd64 1.50.0-1 [7467 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 r-bioc-bsgenome all 1.58.0-1 [7206 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicfeatures all 1.42.1+dfsg-1 [1834 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 r-bioc-variantannotation amd64 1.36.0-1 [3501 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 178 MB in 52s (3434 kB/s) Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6674 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../001-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../006-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../008-libpng16-16_1.6.37-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-libfreetype6_2.10.4+dfsg-1+deb11u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.13.1-4.2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-4.2) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.13.1-4.2_amd64.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libasan6:amd64. Preparing to unpack .../014-libasan6_10.2.1-6_amd64.deb ... Unpacking libasan6:amd64 (10.2.1-6) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../015-libatomic1_10.2.1-6_amd64.deb ... Unpacking libatomic1:amd64 (10.2.1-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../016-libblas3_3.9.0-3+deb11u1_amd64.deb ... Unpacking libblas3:amd64 (3.9.0-3+deb11u1) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../017-libgomp1_10.2.1-6_amd64.deb ... Unpacking libgomp1:amd64 (10.2.1-6) ... Selecting previously unselected package libitm1:amd64. Preparing to unpack .../018-libitm1_10.2.1-6_amd64.deb ... Unpacking libitm1:amd64 (10.2.1-6) ... Selecting previously unselected package liblsan0:amd64. Preparing to unpack .../019-liblsan0_10.2.1-6_amd64.deb ... Unpacking liblsan0:amd64 (10.2.1-6) ... Selecting previously unselected package libtsan0:amd64. 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Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u11) ... Setting up libc6-dev:amd64 (2.31-13+deb11u8) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libstdc++-10-dev:amd64 (10.2.1-6) ... Setting up libboost1.74-dev:amd64 (1.74.0-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up r-cran-bh (1.74.0-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-formatr (1.7-2) ... Setting up r-cran-xml (3.99-0.5-1) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.4-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-curl (4.3+dfsg-1+b1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-matrixstats (0.58.0-3) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-bioc-matrixgenerics (1.2.1-4) ... Setting up r-cran-sys (3.4-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-mime (0.9-1+b1) ... Setting up r-cran-generics (0.1.0-1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-xml2 (1.3.2-1+b1) ... Setting up r-cran-dbi (1.1.1-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-bit (4.0.4+dfsg-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-bitops (1.0-6-5) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.0-1) ... Setting up r-bioc-biobase (2.50.0-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-stringi (1.5.3-1) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-purrr (0.3.4-1+b1) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-cachem (1.0.3-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-openssl (1.4.3+dfsg-2) ... Setting up r-cran-stringr (1.4.0-2) ... Setting up r-bioc-biocparallel (1.24.1-1) ... Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-httr (1.4.2-1) ... Setting up r-cran-memoise (2.0.0-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-tidyselect (1.1.0+dfsg-1) ... Setting up r-cran-hms (1.0.0-1) ... Setting up r-cran-blob (1.2.1-2) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-cran-dplyr (1.0.4-1) ... Setting up r-cran-dbplyr (2.1.0-1) ... Setting up r-cran-rsqlite (2.2.3-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-bioc-biocfilecache (1.14.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.52.0-1) ... Setting up r-bioc-biomart (2.46.2+dfsg-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Setting up r-bioc-rtracklayer (1.50.0-1) ... Setting up r-bioc-genomicfeatures (1.42.1+dfsg-1) ... Setting up r-bioc-bsgenome (1.58.0-1) ... Setting up r-bioc-variantannotation (1.36.0-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation'] 1m27.4s INFO: Running scripts post_install 1m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 1m27.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 1m28.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 1m28.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5icx2hzm to sid 1m28.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m28.8s INFO: Running scripts pre_distupgrade 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_exceptions'] 1m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_exceptions'] 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'update'] 1m33.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9962 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7223 kB] Fetched 17.4 MB in 3s (5046 kB/s) Reading package lists... 1m33.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'update'] 1m33.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-yf', 'dist-upgrade'] 2m24.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-11-base libasan6 libgcc-10-dev libglib2.0-0 libicu67 libldap-2.4-2 libnsl-dev libstdc++-10-dev libtiff5 libtirpc-dev libtsan0 libwebp6 r-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost1.74-dev libcurl4 libdb5.3 libext2fs2 libgnutls30 libhogweed6 libnettle8 libpng16-16 libpsl5 libreadline8 libsemanage1 libssh2-1 libtirpc3 libxt6 The following NEW packages will be installed: fonts-dejavu-mono gcc-11-base gcc-13-base gcc-14-base libapt-pkg6.0t64 libasan8 libboost1.83-dev libcap2 libcurl4t64 libdb5.3t64 libext2fs2t64 libffi8 libfile-find-rule-perl libgcc-13-dev libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libhogweed6t64 libhwasan0 libicu72 libldap-2.5-0 liblerc4 libnettle8t64 libnumber-compare-perl libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 libsemanage2 libsepol2 libsharpyuv0 libssh2-1t64 libssl3t64 libstdc++-13-dev libtext-glob-perl libtiff6 libtirpc3t64 libtsan2 libunistring5 libwebp7 libxt6t64 perl perl-modules-5.38 r-bioc-biocio r-bioc-keggrest r-bioc-s4arrays r-bioc-sparsearray r-cran-abind r-cran-codetools r-cran-cpp11 r-cran-filelock r-cran-png r-cran-restfulr r-cran-rjson r-cran-tidyr r-cran-yaml rpcsvc-proto usrmerge The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gcc-9-base gpgv grep gzip hostname init-system-helpers libacl1 libasan6 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 libcom-err2 libcrypt-dev libcrypt1 libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-s1 libgcrypt20 libgfortran5 libglib2.0-0 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libidn2-0 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libnghttp2-14 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-8-0 libpcre3 libpixman-1-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsmartcols1 libss2 libstdc++-10-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan0 libubsan1 libudev1 libuuid1 libx11-6 libx11-data libxcb-render0 libxcb-shm0 libxcb1 libxext6 libxft2 libxml2 libxrender1 libxxhash0 libzstd1 linux-libc-dev littler login logsave lsb-base mawk mount ncurses-base ncurses-bin node-html5shiv openssl passwd perl-base r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-bit r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-formatr r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgkitten r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 readline-common sed sensible-utils sysvinit-utils tar tzdata ucf unzip util-linux x11-common zip zlib1g zlib1g-dev 234 upgraded, 59 newly installed, 15 to remove and 0 not upgraded. Need to get 246 MB of archives. After this operation, 206 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3 [66.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:6 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [189 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:14 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2 [1643 kB] Get:15 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:21 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:22 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6 [135 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6 [333 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6 [79.7 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6 [33.0 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:37 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:38 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.7.9-2 [2255 kB] Get:39 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240303-1 [42.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240303-1 [72.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-10 [159 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-10 [191 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-10 [117 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-10 [30.1 kB] Get:45 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:46 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-10 [1231 kB] Get:47 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:48 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:49 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:50 http://deb.debian.org/debian sid/main amd64 lsb-base all 11.6 [4584 B] Get:51 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:52 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:53 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:54 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-10 [97.3 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:56 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:57 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:58 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:59 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:60 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:61 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:62 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:64 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:65 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b2 [10.2 kB] Get:67 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240303-1 [713 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13+b1 [984 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:73 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:74 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.9.1-2.2 [328 kB] Get:76 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1 [1425 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:85 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:87 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:88 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:89 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-2 [648 kB] Get:90 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:92 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13+b1 [1368 kB] Get:93 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b2 [19.6 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5+b1 [697 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1 [72.7 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [48.5 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4266 kB] Get:99 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2 [236 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:101 http://deb.debian.org/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:102 http://deb.debian.org/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:103 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:104 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:105 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:106 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-18 [43.5 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240303-1 [136 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240303-1 [25.9 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240303-1 [9208 B] Get:110 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240303-1 [2723 kB] Get:111 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240303-1 [1201 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240303-1 [2455 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240303-1 [1071 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240303-1 [1485 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240303-1 [147 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-18 [2544 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-18 [2211 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:119 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2.1 [10.6 MB] Get:120 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b2 [57.1 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1+b1 [74.1 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.6.0-4 [430 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:127 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:129 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:130 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.3-1 [1669 kB] Get:131 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:132 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:133 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-3 [26.8 MB] Get:134 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b2 [438 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-2 [530 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-3 [278 kB] Get:137 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3.1 [69.2 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-3.1 [167 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:143 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-10 [143 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:149 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:150 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:151 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:152 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:153 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:154 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:155 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:156 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:157 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:160 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:161 http://deb.debian.org/debian sid/main amd64 gcc-11-base amd64 11.4.0-7 [40.3 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libtsan0 amd64 11.4.0-7 [2019 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libasan6 amd64 11.4.0-7 [2049 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libstdc++-10-dev amd64 10.5.0-3 [1755 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libgcc-10-dev amd64 10.5.0-3 [2323 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240303-1 [836 kB] Get:167 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-3 [36.6 kB] Get:168 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.1-1 [129 kB] Get:171 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:172 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:177 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-5 [275 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-5 [1222 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:187 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:188 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:192 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:196 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2.4 [25.0 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:204 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:205 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:206 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:207 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:208 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:209 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:210 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:211 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-13 [230 kB] Get:212 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:213 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.19-1 [99.8 kB] Get:214 http://deb.debian.org/debian sid/main amd64 littler all 0.3.19-1 [15.4 kB] Get:215 http://deb.debian.org/debian sid/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:216 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get:217 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2062 kB] Get:218 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.36.0-1 [2258 kB] Get:219 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.42.0-1 [622 kB] Get:220 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.2.0-1 [484 kB] Get:221 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get:222 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:223 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1+b1 [787 kB] Get:224 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB] Get:225 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3848 kB] Get:226 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1827 kB] Get:227 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.62.0-1 [2119 kB] Get:228 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-5-1 [1394 kB] Get:229 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:230 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:231 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:232 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [504 kB] Get:233 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1196 kB] Get:234 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1794 kB] Get:235 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1139 kB] Get:236 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.7 MB] Get:237 http://deb.debian.org/debian sid/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:238 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:239 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:240 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get:241 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.36.0-1 [1337 kB] Get:242 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3 [1285 kB] Get:243 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1+b1 [3584 kB] Get:244 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.2-1 [824 kB] Get:245 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.16.1-1 [1751 kB] Get:246 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2144 kB] Get:247 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.12.0+dfsg-1 [214 kB] Get:248 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:249 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.8-1 [106 kB] Get:250 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:251 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5094 kB] Get:252 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.70.2-1 [6977 kB] Get:253 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:254 http://deb.debian.org/debian sid/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:255 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.0.8-1 [72.0 kB] Get:256 http://deb.debian.org/debian sid/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:257 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.4-1 [1159 kB] Get:258 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:259 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:260 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:261 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:262 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.3-1 [861 kB] Get:263 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:264 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.0+dfsg-1+b1 [176 kB] Get:265 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:266 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:267 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get:268 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get:269 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.1.1+dfsg-2+b1 [397 kB] Get:270 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:271 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.35-1 [203 kB] Get:272 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:273 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:274 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:275 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:276 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:277 http://deb.debian.org/debian sid/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:278 http://deb.debian.org/debian sid/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get:279 http://deb.debian.org/debian sid/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:280 http://deb.debian.org/debian sid/main amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [301 kB] Get:281 http://deb.debian.org/debian sid/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get:282 http://deb.debian.org/debian sid/main amd64 r-bioc-biomart all 2.58.2+dfsg-1 [450 kB] Get:283 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.54.3+dfsg-1 [1665 kB] Get:284 http://deb.debian.org/debian sid/main amd64 r-bioc-variantannotation amd64 1.48.1-1+b1 [3501 kB] Get:285 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.64.1-1 [4705 kB] Get:286 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:287 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:288 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB] Get:289 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:290 http://deb.debian.org/debian sid/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:291 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:292 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:293 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.12-1 [2071 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 246 MB in 2s (121 MB/s) (Reading database ... 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Installing new version of config file /etc/security/namespace.init ... Installing new version of config file /etc/security/sepermit.conf ... dpkg: libtirpc3:amd64: dependency problems, but removing anyway as you requested: libnsl2:amd64 depends on libtirpc3 (>= 1.0.2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 35268 files and directories currently installed.) Removing libtirpc3:amd64 (1.3.1-1+deb11u1) ... Selecting previously unselected package libtirpc3t64: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 ... 35262 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.1) ... 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Unpacking libgcc-s1:amd64 (14-20240303-1) over (10.2.1-6) ... Setting up libgcc-s1:amd64 (14-20240303-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 36991 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.3-10_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-10) over (2.36.1-8+deb11u1) ... Setting up libblkid1:amd64 (2.39.3-10) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 36995 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-10_amd64.deb ... Unpacking bsdutils (1:2.39.3-10) over (1:2.36.1-8+deb11u1) ... Setting up bsdutils (1:2.39.3-10) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 36996 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3.1_amd64.deb ... Unpacking coreutils (9.4-3.1) over (8.32-4+b1) ... Setting up coreutils (9.4-3.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37001 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.8.0-1) ... Setting up findutils (4.9.0-5) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37001 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37002 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271+b2_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271+b2) over (0.260) ... Setting up libdebconfclient0:amd64 (0.271+b2) ... (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 ... 37003 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_amd64.deb ... Unpacking base-passwd (3.6.3) over (3.5.51) ... Setting up base-passwd (3.6.3) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37003 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.2.4) ... Selecting previously unselected package libapt-pkg6.0t64: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 ... 36954 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.13+b1_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.13+b1) ... Setting up libapt-pkg6.0t64:amd64 (2.7.13+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37005 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37005 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1+b1_amd64.deb ... Unpacking libudev1:amd64 (255.4-1+b1) over (247.3-7+deb11u4) ... Setting up libudev1:amd64 (255.4-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37007 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2+b1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.2-2+b1) over (0.8.0-2) ... Setting up libxxhash0:amd64 (0.8.2-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37008 files and directories currently installed.) Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) over (1:1.2.11.dfsg-2+deb11u2) ... Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1) over (1:1.2.11.dfsg-2+deb11u2) ... Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: librtmp1:amd64 depends on libhogweed6. libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (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 ... 37011 files and directories currently installed.) Removing libhogweed6:amd64 (3.7.3-1) ... Selecting previously unselected package libhogweed6t64: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 ... 37005 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2+b3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) over (2.4+20151223.gitfa8646d.1-2+b2) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libnettle8 (>= 3.7~). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37012 files and directories currently installed.) Removing libnettle8:amd64 (3.7.3-1) ... Selecting previously unselected package libnettle8t64: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 ... 37004 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2_amd64.deb ... Unpacking libnettle8t64:amd64 (3.9.1-2.2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37018 files and directories currently installed.) Preparing to unpack .../libunistring5_1.1-2_amd64.deb ... Unpacking libunistring5:amd64 (1.1-2) ... Setting up libunistring5:amd64 (1.1-2) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: libldap-2.4-2:amd64 depends on libgnutls30 (>= 3.7.0). apt depends on libgnutls30 (>= 3.7.0). (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 ... 37024 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.1-5+deb11u4) ... Selecting previously unselected package libgnutls30t64: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 ... 36997 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.3-1.1) ... Setting up libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libgnutls30t64:amd64 (3.8.3-1.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37026 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37028 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3+b2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3+b2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-3+b2) ... (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 ... 37029 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.1-1) ... Setting up libsemanage-common (3.5-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2: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 ... 37029 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_amd64.deb ... Unpacking libsepol2:amd64 (3.5-2) ... Setting up libsepol2:amd64 (3.5-2) ... Selecting previously unselected package libsemanage2: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 ... 37033 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b2_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b2) ... Setting up libsemanage2:amd64 (3.5-1+b2) ... (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 ... 37038 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-4) over (1:4.8.1-1) ... Setting up passwd (1:4.13+dfsg1-4) ... Installing new version of config file /etc/default/useradd ... (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 ... 37072 files and directories currently installed.) Removing libsemanage1:amd64 (3.1-1+b2) ... (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 ... 37067 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.137) over (3.118+deb11u1) ... Setting up adduser (3.137) ... Installing new version of config file /etc/deluser.conf ... (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 ... 37029 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-2_amd64.deb ... Unpacking gpgv (2.2.40-2) over (2.2.27-2+deb11u2) ... Setting up gpgv (2.2.40-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37029 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.4_all.deb ... Unpacking debian-archive-keyring (2023.4) over (2021.1.1+deb11u1) ... Setting up debian-archive-keyring (2023.4) ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (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 ... 37029 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1) over (2.5.1-1+deb11u1) ... Setting up libseccomp2:amd64 (2.5.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37029 files and directories currently installed.) Preparing to unpack .../apt_2.7.13+b1_amd64.deb ... Unpacking apt (2.7.13+b1) over (2.2.4) ... Setting up apt (2.7.13+b1) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Removing obsolete conffile /etc/kernel/postinst.d/apt-auto-removal ... Selecting previously unselected package perl-modules-5.38. (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 ... 37023 files and directories currently installed.) Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-4+b2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b2) over (2.1.27+dfsg-2.1+deb11u1) ... (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 ... 38436 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg1-0.8) ... Selecting previously unselected package libdb5.3t64: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 ... 38430 files and directories currently installed.) Preparing to unpack .../0-libdb5.3t64_5.3.28+dfsg2-5+b1_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-5+b1) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.23-5.1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.23-5.1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../3-libperl5.38t64_5.38.2-3.2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.38.2-3.2_amd64.deb ... Unpacking perl (5.38.2-3.2) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../5-libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (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 ... 39044 files and directories currently installed.) Preparing to unpack .../libtext-glob-perl_0.11-3_all.deb ... Unpacking libtext-glob-perl (0.11-3) ... Setting up libtext-glob-perl (0.11-3) ... Selecting previously unselected package libfile-find-rule-perl. (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 ... 39051 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-5+b1) ... Setting up libgdbm6t64:amd64 (1.23-5.1) ... Setting up libgdbm-compat4t64:amd64 (1.23-5.1) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2) ... Setting up perl (5.38.2-3.2) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 39066 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_39_all.deb ... Unpacking usrmerge (39) ... Setting up usrmerge (39) ... (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 ... 39073 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.60) ... Setting up init-system-helpers (1.66) ... (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 ... 39073 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-base (6.4+20240113-1) ... Selecting previously unselected package gcc-13-base: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 ... 39073 files and directories currently installed.) Preparing to unpack .../00-gcc-13-base_13.2.0-18_amd64.deb ... Unpacking gcc-13-base:amd64 (13.2.0-18) ... Preparing to unpack .../01-libgomp1_14-20240303-1_amd64.deb ... Unpacking libgomp1:amd64 (14-20240303-1) over (10.2.1-6) ... Preparing to unpack .../02-libitm1_14-20240303-1_amd64.deb ... Unpacking libitm1:amd64 (14-20240303-1) over (10.2.1-6) ... Preparing to unpack .../03-libatomic1_14-20240303-1_amd64.deb ... Unpacking libatomic1:amd64 (14-20240303-1) over (10.2.1-6) ... Selecting previously unselected package libasan8:amd64. Preparing to unpack .../04-libasan8_14-20240303-1_amd64.deb ... Unpacking libasan8:amd64 (14-20240303-1) ... Preparing to unpack .../05-liblsan0_14-20240303-1_amd64.deb ... Unpacking liblsan0:amd64 (14-20240303-1) over (10.2.1-6) ... Selecting previously unselected package libtsan2:amd64. Preparing to unpack .../06-libtsan2_14-20240303-1_amd64.deb ... Unpacking libtsan2:amd64 (14-20240303-1) ... Preparing to unpack .../07-libubsan1_14-20240303-1_amd64.deb ... Unpacking libubsan1:amd64 (14-20240303-1) over (10.2.1-6) ... Selecting previously unselected package libhwasan0:amd64. Preparing to unpack .../08-libhwasan0_14-20240303-1_amd64.deb ... Unpacking libhwasan0:amd64 (14-20240303-1) ... Preparing to unpack .../09-libquadmath0_14-20240303-1_amd64.deb ... Unpacking libquadmath0:amd64 (14-20240303-1) over (10.2.1-6) ... Selecting previously unselected package libgcc-13-dev:amd64. Preparing to unpack .../10-libgcc-13-dev_13.2.0-18_amd64.deb ... Unpacking libgcc-13-dev:amd64 (13.2.0-18) ... Selecting previously unselected package libstdc++-13-dev:amd64. Preparing to unpack .../11-libstdc++-13-dev_13.2.0-18_amd64.deb ... Unpacking libstdc++-13-dev:amd64 (13.2.0-18) ... Preparing to unpack .../12-libboost-dev_1.83.0.2+b2_amd64.deb ... Unpacking libboost-dev:amd64 (1.83.0.2+b2) over (1.74.0.3) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 24621 files and directories currently installed.) Preparing to unpack .../libboost1.83-dev_1.83.0-2.1_amd64.deb ... Unpacking libboost1.83-dev:amd64 (1.83.0-2.1) ... Preparing to unpack .../libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b2) ... Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-4+b2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-4+b2) over (2.1.27+dfsg-2.1+deb11u1) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../libldap-2.5-0_2.5.16+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Preparing to unpack .../libnghttp2-14_1.59.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1+b1) over (1.43.0-1+deb11u1) ... dpkg: libcurl4:amd64: dependency problems, but removing anyway as you requested: r-cran-rcurl depends on libcurl4 (>= 7.16.2). r-cran-curl depends on libcurl4 (>= 7.28.0). r-bioc-variantannotation depends on libcurl4 (>= 7.18.0). r-bioc-rsamtools depends on libcurl4 (>= 7.18.0). r-bioc-rhtslib depends on libcurl4 (>= 7.18.0). r-base-core depends on libcurl4 (>= 7.28.0). (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.0-2.4) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up libext2fs2t64:amd64 (1.47.0-2.4) ... (Reading database ... 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Unpacking e2fsprogs (1.47.0-2.4) over (1.46.2-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../1-r-cran-rlang_1.1.3-1_amd64.deb ... Unpacking r-cran-rlang (1.1.3-1) over (0.4.10-1) ... Preparing to unpack .../2-r-cran-pillar_1.9.0+dfsg-1_all.deb ... Unpacking r-cran-pillar (1.9.0+dfsg-1) over (1.4.7-1) ... Preparing to unpack .../3-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... Unpacking r-cran-tibble (3.2.1+dfsg-2) over (3.0.6+dfsg-1) ... Preparing to unpack .../4-r-base-core_4.3.3-3_amd64.deb ... Unpacking r-base-core (4.3.3-3) over (4.0.4-1) ... Preparing to unpack .../5-libfreetype6_2.13.2+dfsg-1+b2_amd64.deb ... 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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 (8.2-3.1) ... Preparing to unpack .../libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) over (2:1.7.2-1+deb11u2) ... Preparing to unpack .../libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) over (1.14-3) ... Preparing to unpack .../libx11-6_2%3a1.8.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1) over (2:1.7.2-1+deb11u2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41395 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-15+b1_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15+b1) over (2:8.39-13) ... Setting up libpcre3:amd64 (2:8.39-15+b1) ... (Reading database ... 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Processing triggers for debianutils (5.17) ... Processing triggers for libc-bin (2.37-15.1) ... 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. 2m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-yf', 'dist-upgrade'] 2m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m25.7s DUMP: c38edf595f39d24d2439202f182978b8 - 2m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-variantannotation'] 2m26.0s DUMP: Package: r-bioc-variantannotation Source: r-bioc-variantannotation (1.48.1-1) Version: 1.48.1-1+b1 Installed-Size: 6117 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-biocgenerics (>= 0.37.0), r-bioc-matrixgenerics, r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.41.5), r-bioc-summarizedexperiment (>= 1.19.5), r-bioc-rsamtools (>= 1.99.0), r-cran-dbi, r-bioc-zlibbioc, r-bioc-biobase, r-bioc-s4vectors (>= 0.27.12), r-bioc-iranges (>= 2.23.9), r-bioc-xvector (>= 0.29.2), r-bioc-biostrings (>= 2.57.2), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), r-bioc-rhtslib (>= 1.99.3), libbz2-1.0, libc6 (>= 2.34), libcurl4t64 (>= 7.18.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.2.3.3) Suggests: r-cran-runit, r-bioc-annotationhub, r-bioc-snpstats, r-cran-ggplot2, r-bioc-biocstyle, r-cran-knitr Description-en: BioConductor annotation of genetic variants This BioConductor package provides R functions to annotate variants, compute amino acid coding changess and to predict coding outcomes. Description-md5: 17670e83de551a30abddcb85706e9bf5 Homepage: https://bioconductor.org/packages/VariantAnnotation/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.48.1-1+b1_amd64.deb Size: 3500564 MD5sum: 6f6d6fe3baa9a36a47f29706a786d521 SHA256: 8e3f16105e3c4d919b8327da51d9694a888739b5fbfeafda8acf2dab7e37ea96 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-variantannotation'] 2m26.0s INFO: apt-cache knows about the following packages: r-bioc-variantannotation 2m26.0s INFO: Running scripts pre_install 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 2m26.1s 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: 2m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 2m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 2m26.2s DUMP: r-bioc-variantannotation: Installed: 1.48.1-1+b1 Candidate: 1.48.1-1+b1 Version table: *** 1.48.1-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 2m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation'] 2m26.8s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-variantannotation is already the newest version (1.48.1-1+b1). The following packages were automatically installed and are no longer required: gcc-11-base libasan6 libgcc-10-dev libglib2.0-0 libicu67 libldap-2.4-2 libnsl-dev libstdc++-10-dev libtiff5 libtirpc-dev libtsan0 libwebp6 r-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation'] 2m26.8s INFO: Running scripts post_install 2m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 2m26.8s INFO: Running scripts post_distupgrade 2m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_exceptions'] 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_exceptions'] 2m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_zz_backports'] 2m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_distupgrade_zz_backports'] 2m26.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m28.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m28.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m29.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m29.5s INFO: Running scripts pre_install 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_database-server'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_exceptions'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_extras'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 2m29.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy'] 2m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 2m29.6s DUMP: r-bioc-variantannotation: Installed: 1.48.1-1+b1 Candidate: 1.48.1-1+b1 Version table: *** 1.48.1-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-cache', 'policy', 'r-bioc-variantannotation'] 2m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation=1.48.1-1+b1'] 2m30.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-variantannotation is already the newest version (1.48.1-1+b1). The following packages were automatically installed and are no longer required: gcc-11-base libasan6 libgcc-10-dev libglib2.0-0 libicu67 libldap-2.4-2 libnsl-dev libstdc++-10-dev libtiff5 libtirpc-dev libtsan0 libwebp6 r-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', 'install', 'r-bioc-variantannotation=1.48.1-1+b1'] 2m30.4s INFO: Running scripts post_install 2m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 2m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_install_exceptions'] 2m30.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m32.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m32.0s INFO: /bin converted to /usr/bin by /usr merge 2m32.1s INFO: /lib converted to /usr/lib by /usr merge 2m32.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m32.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m32.1s INFO: /sbin converted to /usr/sbin by /usr merge 2m34.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', '-ac', '--ignore-obsolete'] 2m38.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', '-ac', '--ignore-obsolete'] 2m38.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m38.6s DUMP: 0.15.6 2m38.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m38.6s INFO: Running adequate version 0.15.6 now. 2m38.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'r-bioc-variantannotation'] 2m38.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'r-bioc-variantannotation'] 2m38.7s INFO: Running scripts pre_remove 2m38.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_exceptions'] 2m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/pre_remove_exceptions'] 2m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m45.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.13+b1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-10 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-11-base:amd64 gcc-11-base 11.4.0-7 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-18 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240303-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libasan6:amd64 libasan6 11.4.0-7 install ok installed libasan8:amd64 libasan8 14-20240303-1 install ok installed libatomic1:amd64 libatomic1 14-20240303-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-10 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-2.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc-dev-bin libc-dev-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libc6-dev:amd64 libc6-dev 2.37-15.1 install ok installed libcairo2:amd64 libcairo2 1.18.0-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl4t64:amd64 libcurl4t64 8.6.0-4 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b2 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b2 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-10-dev:amd64 libgcc-10-dev 10.5.0-3 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-18 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240303-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1 install ok installed libgfortran5:amd64 libgfortran5 14-20240303-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-5 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgomp1:amd64 libgomp1 14-20240303-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhwasan0:amd64 libhwasan0 14-20240303-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libitm1:amd64 libitm1 14-20240303-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblsan0:amd64 liblsan0 14-20240303-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-10 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1+b1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.1+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.1+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.1+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15+b1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-3 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libquadmath0:amd64 libquadmath0 14-20240303-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-3.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-10 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++-10-dev:amd64 libstdc++-10-dev 10.5.0-3 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-18 install ok installed libstdc++6:amd64 libstdc++6 14-20240303-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.1 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.1 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtsan0:amd64 libtsan0 11.4.0-7 install ok installed libtsan2:amd64 libtsan2 14-20240303-1 install ok installed libubsan1:amd64 libubsan1 14-20240303-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-10 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.7.9-2 install ok installed littler littler 0.3.19-1 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed lsb-base lsb-base 11.6 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-10 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed r-base-core r-base-core 4.3.3-3 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.64.1-1 install ok installed r-bioc-biobase r-bioc-biobase 2.62.0-1 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.10.1+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.48.1-2 install ok installed r-bioc-biocio r-bioc-biocio 1.12.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.36.0-1 install ok installed r-bioc-biomart r-bioc-biomart 2.58.2+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.70.2+dfsg-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.70.2-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.28.0+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.38.6+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.11-2 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.38.2-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.54.3+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.54.1+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.36.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.42.0+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.14.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.4.1+dfsg-3 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.18.0+dfsg-1+b1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.62.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.2.0+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.40.2+dfsg-1 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.2.4+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.32.0+dfsg-1 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.48.1-1+b1 install ok installed r-bioc-xvector r-bioc-xvector 0.42.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.48.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 install ok installed r-cran-askpass r-cran-askpass 1.2.0-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-cachem r-cran-cachem 1.0.8-1 install ok installed r-cran-cli r-cran-cli 3.6.2-1 install ok installed r-cran-codetools r-cran-codetools 0.2-19-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.4.7-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.2.0+dfsg-1+b1 install ok installed r-cran-dbi r-cran-dbi 1.2.2-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.4.0+dfsg-1 install ok installed r-cran-digest r-cran-digest 0.6.35-1 install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-filelock r-cran-filelock 1.0.3-1 install ok installed r-cran-formatr r-cran-formatr 1.14-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.22-5-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.19-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-matrix r-cran-matrix 1.6-5-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.2.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-openssl r-cran-openssl 2.1.1+dfsg-2+b1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.12-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.14+dfsg-1+b1 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.1.3-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.4-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-stringi r-cran-stringi 1.8.3-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-sys r-cran-sys 3.4.2-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.16.1-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.6-1 install ok installed r-cran-yaml r-cran-yaml 2.3.8-1 install ok installed readline-common readline-common 8.2-3.1 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.22 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-10 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3.1 2m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'libtirpc3:amd64=1.3.4+ds-1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'gcc-11-base:amd64-', 'gcc-13-base:amd64-', 'libasan6:amd64-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-10-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhogweed6t64:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libitm1:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblsan0:amd64-', 'libnettle8t64:amd64-', 'libnghttp2-14:amd64-', 'libnsl-dev:amd64-', 'libpango-1.0-0:amd64-', 'libpangocairo-1.0-0:amd64-', 'libpangoft2-1.0-0:amd64-', 'libpaper-utils-', 'libpaper1:amd64-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-10-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libtsan0:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'littler-', 'node-html5shiv-', 'openssl-', 'r-base-core-', 'r-bioc-annotationdbi-', 'r-bioc-biobase-', 'r-bioc-biocfilecache-', 'r-bioc-biocgenerics-', 'r-bioc-biocio-', 'r-bioc-biocparallel-', 'r-bioc-biomart-', 'r-bioc-biostrings-', 'r-bioc-bsgenome-', 'r-bioc-delayedarray-', 'r-bioc-genomeinfodb-', 'r-bioc-genomeinfodbdata-', 'r-bioc-genomicalignments-', 'r-bioc-genomicfeatures-', 'r-bioc-genomicranges-', 'r-bioc-iranges-', 'r-bioc-keggrest-', 'r-bioc-matrixgenerics-', 'r-bioc-rhtslib-', 'r-bioc-rsamtools-', 'r-bioc-rtracklayer-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-summarizedexperiment-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-askpass-', 'r-cran-assertthat-', '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-dbplyr-', 'r-cran-digest-', 'r-cran-dplyr-', 'r-cran-ellipsis-', 'r-cran-fansi-', 'r-cran-fastmap-', 'r-cran-filelock-', 'r-cran-formatr-', 'r-cran-futile.logger-', 'r-cran-futile.options-', 'r-cran-generics-', 'r-cran-glue-', 'r-cran-hms-', 'r-cran-httr-', 'r-cran-jsonlite-', 'r-cran-lambda.r-', 'r-cran-lattice-', 'r-cran-lifecycle-', 'r-cran-littler-', 'r-cran-magrittr-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'r-cran-memoise-', 'r-cran-mime-', 'r-cran-openssl-', 'r-cran-pillar-', 'r-cran-pkgconfig-', 'r-cran-pkgkitten-', 'r-cran-plogr-', 'r-cran-png-', 'r-cran-prettyunits-', 'r-cran-progress-', 'r-cran-purrr-', 'r-cran-r6-', 'r-cran-rappdirs-', 'r-cran-rcpp-', 'r-cran-rcurl-', 'r-cran-restfulr-', 'r-cran-rjson-', 'r-cran-rlang-', 'r-cran-rsqlite-', 'r-cran-snow-', 'r-cran-stringi-', 'r-cran-stringr-', 'r-cran-sys-', 'r-cran-tibble-', 'r-cran-tidyr-', 'r-cran-tidyselect-', 'r-cran-utf8-', 'r-cran-vctrs-', 'r-cran-withr-', 'r-cran-xml-', 'r-cran-xml2-', 'r-cran-yaml-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-variantannotation-'] 2m49.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gcc-11-base gcc-13-base libasan6 libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgcc-13-dev libgfortran5 libglib2.0-0 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libhogweed6t64 libhwasan0 libice6 libicu67 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-jquery liblapack3 libldap-2.4-2 libldap-2.5-0 liblerc4 liblsan0 libnettle8t64 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-10-dev libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff5 libtiff6 libtirpc-dev libtirpc3t64 libtk8.6 libtsan0 libtsan2 libubsan1 libwebp6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat 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-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev The following NEW packages will be installed: libhogweed6 libnettle8 libtirpc3 0 upgraded, 3 newly installed, 206 to remove and 0 not upgraded. Need to get 705 kB of archives. After this operation, 652 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2+b1 [328 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2+b1 [296 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 705 kB in 0s (7168 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41505 files and directories currently installed.) Removing r-bioc-variantannotation (1.48.1-1+b1) ... Removing r-bioc-genomicfeatures (1.54.3+dfsg-1) ... Removing r-bioc-biomart (2.58.2+dfsg-1) ... Removing r-bioc-biocfilecache (2.10.1+dfsg-1) ... Removing r-cran-dbplyr (2.4.0+dfsg-1) ... Removing libstdc++-10-dev:amd64 (10.5.0-3) ... Removing libgcc-10-dev:amd64 (10.5.0-3) ... Removing libtsan0:amd64 (11.4.0-7) ... Removing libasan6:amd64 (11.4.0-7) ... Removing gcc-11-base:amd64 (11.4.0-7) ... Removing r-bioc-annotationdbi (1.64.1-1) ... Removing r-bioc-keggrest (1.42.0+dfsg-1) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-curl (5.2.0+dfsg-1+b1) ... Removing r-bioc-bsgenome (1.70.2-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libglib2.0-0:amd64 (2.78.4-5) ... Removing r-bioc-rtracklayer (1.62.0-1) ... Removing r-bioc-genomicalignments (1.38.2-1) ... Removing r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... Removing r-bioc-delayedarray (0.28.0+dfsg-1) ... Removing r-bioc-sparsearray (1.2.4+dfsg-1) ... Removing r-bioc-s4arrays (1.2.0+dfsg-1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-bioc-rsamtools (2.18.0+dfsg-1+b1) ... Removing r-bioc-biocparallel (1.36.0-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-2.1) ... Removing libstdc++-13-dev:amd64 (13.2.0-18) ... Removing libgcc-13-dev:amd64 (13.2.0-18) ... Removing gcc-13-base:amd64 (13.2.0-18) ... Removing libasan8:amd64 (14-20240303-1) ... Removing libatomic1:amd64 (14-20240303-1) ... Removing r-bioc-biostrings (2.70.2+dfsg-1) ... Removing r-bioc-genomicranges (1.54.1+dfsg-1) ... Removing r-bioc-xvector (0.42.0-1) ... Removing r-bioc-rhtslib (2.4.1+dfsg-3) ... Removing r-bioc-zlibbioc (1.48.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libc6-dev:amd64 (2.37-15.1) ... Removing libc-dev-bin (2.37-15.1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... dpkg: libexpat1:amd64: dependency problems, but removing anyway as you requested: libfontconfig1:amd64 depends on libexpat1 (>= 2.0.1). Removing libexpat1:amd64 (2.6.2-1) ... dpkg: libfribidi0:amd64: dependency problems, but removing anyway as you requested: libpango-1.0-0:amd64 depends on libfribidi0 (>= 1.0.0). Removing libfribidi0:amd64 (1.0.13-3+b1) ... dpkg: libgfortran5:amd64: dependency problems, but removing anyway as you requested: liblapack3:amd64 depends on libgfortran5 (>= 8). Removing libgfortran5:amd64 (14-20240303-1) ... dpkg: libglib2.0-0t64:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libglib2.0-0t64 (>= 2.12.0). libpangoft2-1.0-0:amd64 depends on libglib2.0-0t64 (>= 2.68.0). libpangocairo-1.0-0:amd64 depends on libglib2.0-0t64 (>= 2.56.0). libpango-1.0-0:amd64 depends on libglib2.0-0t64 (>= 2.75.3). libharfbuzz0b:amd64 depends on libglib2.0-0t64 (>= 2.32.0). Removing libglib2.0-0t64:amd64 (2.78.4-5) ... dpkg: libgomp1:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libgomp1 (>= 4.9). Removing libgomp1:amd64 (14-20240303-1) ... dpkg: libgraphite2-3:amd64: dependency problems, but removing anyway as you requested: libharfbuzz0b:amd64 depends on libgraphite2-3 (>= 1.2.2). Removing libgraphite2-3:amd64 (1.3.14-2) ... dpkg: librtmp1:amd64: dependency problems, but removing anyway as you requested: libcurl4t64:amd64 depends on librtmp1 (>= 2.3). Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... dpkg: r-cran-tidyselect: dependency problems, but removing anyway as you requested: r-cran-tidyr depends on r-cran-tidyselect (>= 1.2.0). r-cran-dplyr depends on r-cran-tidyselect (>= 1.2.0). Removing r-cran-tidyselect (1.2.0+dfsg-1) ... dpkg: r-base-core: dependency problems, but removing anyway as you requested: r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-sys depends on r-base-core (>= 4.3.1-1). r-cran-sys depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rjson depends on r-base-core (>= 4.1.2-1). r-cran-rjson depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-restfulr depends on r-base-core (>= 4.2.1-1). r-cran-restfulr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rappdirs depends on r-base-core (>= 4.0.3-1). r-cran-rappdirs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-plogr depends on r-base-core (>= 4.0.0-3). r-cran-plogr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgkitten depends on r-base-core (>= 4.2.2.20221110-2). r-cran-pkgkitten depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mime depends on r-base-core (>= 4.2.1-2). r-cran-mime depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-memoise depends on r-base-core (>= 4.1.2-1). r-cran-memoise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-littler depends on r-base-core (>= 4.3.2-1). r-cran-littler depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lambda.r depends on r-base-core (>= 4.0.0-3). r-cran-lambda.r depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-hms depends on r-base-core (>= 4.3.1-1). r-cran-hms depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-generics depends on r-base-core (>= 4.2.1-1). r-cran-generics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.options depends on r-base-core (>= 4.0.0-3). r-cran-futile.options depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.logger depends on r-base-core (>= 4.0.0-3). r-cran-futile.logger depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-formatr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-formatr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fastmap depends on r-base-core (>= 4.2.2.20221110-2). r-cran-fastmap depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-codetools depends on r-base-core (>= 4.2.2.20221110-2). r-cran-codetools depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cachem depends on r-base-core (>= 4.3.0-1). r-cran-cachem depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-blob depends on r-base-core (>= 4.3.0-1). r-cran-blob depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bitops depends on r-base-core (>= 4.1.1-2). r-cran-bitops depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit64 depends on r-base-core (>= 4.0.2-1). r-cran-bit64 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit depends on r-base-core (>= 4.2.2.20221110-1). r-cran-bit depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-yaml depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-xml2 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-xml depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-withr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-vctrs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-utf8 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tidyr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-tibble depends on r-base-core (>= 4.3.1-2). r-cran-tibble depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-sys depends on r-base-core (>= 4.3.1-1). r-cran-sys depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-stringr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-stringi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rsqlite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rlang depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rjson depends on r-base-core (>= 4.1.2-1). r-cran-rjson depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-restfulr depends on r-base-core (>= 4.2.1-1). r-cran-restfulr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rcurl depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rcpp depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-rappdirs depends on r-base-core (>= 4.0.3-1). r-cran-rappdirs depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-r6 depends on r-base-core (>= 4.1.1-2). r-cran-r6 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-purrr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-progress depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-prettyunits depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-png depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-plogr depends on r-base-core (>= 4.0.0-3). r-cran-plogr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgkitten depends on r-base-core (>= 4.2.2.20221110-2). r-cran-pkgkitten depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pkgconfig depends on r-base-core (>= 4.0.0-3). r-cran-pkgconfig depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-pillar depends on r-base-core (>= 4.3.0-1). r-cran-pillar depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-openssl depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-mime depends on r-base-core (>= 4.2.1-2). r-cran-mime depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-memoise depends on r-base-core (>= 4.1.2-1). r-cran-memoise depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-matrixstats depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-magrittr depends on r-base-core (>= 4.2.0-1). r-cran-magrittr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-littler depends on r-base-core (>= 4.3.2-1). r-cran-littler depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lifecycle depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lattice depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-lambda.r depends on r-base-core (>= 4.0.0-3). r-cran-lambda.r depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-jsonlite depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-hms depends on r-base-core (>= 4.3.1-1). r-cran-hms depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-glue depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-generics depends on r-base-core (>= 4.2.1-1). r-cran-generics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.options depends on r-base-core (>= 4.0.0-3). r-cran-futile.options depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-futile.logger depends on r-base-core (>= 4.0.0-3). r-cran-futile.logger depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-formatr depends on r-base-core (>= 4.2.2.20221110-1). r-cran-formatr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-filelock depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fastmap depends on r-base-core (>= 4.2.2.20221110-2). r-cran-fastmap depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-fansi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-ellipsis depends on r-base-core (>= 4.1.1-2). r-cran-ellipsis depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-dplyr depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-digest depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-dbi depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-crayon depends on r-base-core (>= 4.2.1-2). r-cran-crayon depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cpp11 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-codetools depends on r-base-core (>= 4.2.2.20221110-2). r-cran-codetools depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cli depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-cachem depends on r-base-core (>= 4.3.0-1). r-cran-cachem depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-blob depends on r-base-core (>= 4.3.0-1). r-cran-blob depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bitops depends on r-base-core (>= 4.1.1-2). r-cran-bitops depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit64 depends on r-base-core (>= 4.0.2-1). r-cran-bit64 depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-bit depends on r-base-core (>= 4.2.2.20221110-1). r-cran-bit depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-assertthat depends on r-base-core (>= 4.0.0-3). r-cran-assertthat depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-cran-askpass depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-s4vectors depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-matrixgenerics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-iranges depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-genomeinfodbdata depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-genomeinfodb depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biocio depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biocgenerics depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. r-bioc-biobase depends on r-api-4.0; however: Package r-api-4.0 is not installed. Package r-base-core which provides r-api-4.0 is to be removed. Removing r-base-core (4.3.3-3) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.1+ds-1) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo2:amd64 (1.18.0-2) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b2) ... dpkg: libcurl4t64:amd64: dependency problems, but removing anyway as you requested: r-cran-rcurl depends on libcurl4t64 (>= 7.16.2). Removing libcurl4t64:amd64 (8.6.0-4) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libxss1:amd64 (1:1.2.3-1) ... dpkg: libx11-6:amd64: dependency problems, but removing anyway as you requested: libxrender1:amd64 depends on libx11-6 (>= 2:1.6.0). libxext6:amd64 depends on libx11-6 (>= 2:1.6.0). Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... dpkg: libxcb1:amd64: dependency problems, but removing anyway as you requested: libxcb-render0:amd64 depends on libxcb1 (>= 1.8). Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libbsd0:amd64 (0.12.1-1) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Selecting previously unselected package libhogweed6: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 ... 17747 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2+b1_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2+b1) ... Replaced by files in installed package libhogweed6t64:amd64 (3.9.1-2.2) ... dpkg: libhogweed6t64:amd64: dependency problems, but removing anyway as you requested: libgnutls30t64:amd64 depends on libhogweed6 (>= 3.6); however: Package libhogweed6:amd64 is not configured yet. Package libhogweed6t64:amd64 which provides libhogweed6 is to be removed. (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 ... 17752 files and directories currently installed.) Removing libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6:amd64 (3.9.1-2+b1) ... Selecting previously unselected package libnettle8: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 ... 17745 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2+b1_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2+b1) ... Replaced by files in installed package libnettle8t64:amd64 (3.9.1-2.2) ... dpkg: libnettle8t64:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8; however: Package libnettle8:amd64 is not configured yet. Package libnettle8t64:amd64 which provides libnettle8 is to be removed. libgnutls30t64:amd64 depends on libnettle8 (>= 3.9~); however: Package libnettle8:amd64 is not configured yet. Package libnettle8t64:amd64 which provides libnettle8 is to be removed. (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 ... 17752 files and directories currently installed.) Removing libnettle8t64:amd64 (3.9.1-2.2) ... Setting up libnettle8:amd64 (3.9.1-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17743 files and directories currently installed.) Removing libhwasan0:amd64 (14-20240303-1) ... Removing libicu67:amd64 (67.1-7) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.3-1) ... Removing r-cran-xml2 (1.3.6-1) ... Removing libitm1:amd64 (14-20240303-1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing liblsan0:amd64 (14-20240303-1) ... Removing libnghttp2-14:amd64 (1.59.0-1+b1) ... Removing libnsl-dev:amd64 (1.3.0-3) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing r-cran-png (0.1-8-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libquadmath0:amd64 (14-20240303-1) ... Removing libreadline8t64:amd64 (8.2-3.1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b2) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b2) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.1) ... dpkg: libxml2:amd64: dependency problems, but removing anyway as you requested: r-cran-xml depends on libxml2 (>= 2.7.4). Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... dpkg: libtirpc3t64:amd64: dependency problems, but removing anyway as you requested: libnsl2:amd64 depends on libtirpc3 (>= 1.0.2); however: Package libtirpc3 is not installed. Package libtirpc3t64:amd64 which provides libtirpc3 is to be removed. Removing libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Selecting previously unselected package libtirpc3: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 ... 16746 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.4+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.4+ds-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 16753 files and directories currently installed.) Removing libtsan2:amd64 (14-20240303-1) ... Removing libubsan1:amd64 (14-20240303-1) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-xml (3.99-0.16.1-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing linux-libc-dev (6.7.9-2) ... Removing r-cran-rcpp (1.0.12-1) ... Removing littler (0.3.19-1) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing openssl (3.1.5-1.1) ... Removing r-bioc-biobase (2.62.0-1) ... Removing r-bioc-genomeinfodb (1.38.6+dfsg-1) ... Removing r-bioc-iranges (2.36.0-1) ... Removing r-bioc-biocio (1.12.0+dfsg-1) ... Removing r-bioc-s4vectors (0.40.2+dfsg-1) ... Removing r-bioc-matrixgenerics (1.14.0-1) ... Removing r-bioc-biocgenerics (0.48.1-2) ... Removing r-bioc-genomeinfodbdata (1.2.11-2) ... Removing r-cran-openssl (2.1.1+dfsg-2+b1) ... Removing r-cran-askpass (1.2.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-rsqlite (2.3.4-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.8-1) ... Removing r-cran-dplyr (1.1.4-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-cpp11 (0.4.7-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-dbi (1.2.2-1) ... Removing r-cran-digest (0.6.35-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-1) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-lattice (0.22-5-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-littler (0.3.19-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-matrixstats (1.2.0-1) ... Removing r-cran-mime (0.12-1+b1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sys (3.4.2-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing r-cran-yaml (2.3.8-1) ... Removing readline-common (8.2-3.1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.22) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-rlang (1.1.3-1) ... Removing r-cran-cli (3.6.2-1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 2m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'libtirpc3:amd64=1.3.4+ds-1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'gcc-11-base:amd64-', 'gcc-13-base:amd64-', 'libasan6:amd64-', 'libasan8:amd64-', 'libatomic1:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgcc-10-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libharfbuzz0b:amd64-', 'libhogweed6t64:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu67:amd64-', 'libicu72:amd64-', 'libitm1:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'liblapack3:amd64-', 'libldap-2.4-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'liblsan0:amd64-', 'libnettle8t64:amd64-', 'libnghttp2-14:amd64-', 'libnsl-dev:amd64-', 'libpango-1.0-0:amd64-', 'libpangocairo-1.0-0:amd64-', 'libpangoft2-1.0-0:amd64-', 'libpaper-utils-', 'libpaper1:amd64-', 'libpixman-1-0:amd64-', 'libpng16-16t64:amd64-', 'libpsl5t64:amd64-', 'libquadmath0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libssh2-1t64:amd64-', 'libstdc++-10-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff5:amd64-', 'libtiff6:amd64-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libtsan0:amd64-', 'libtsan2:amd64-', 'libubsan1:amd64-', 'libwebp6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxml2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'littler-', 'node-html5shiv-', 'openssl-', 'r-base-core-', 'r-bioc-annotationdbi-', 'r-bioc-biobase-', 'r-bioc-biocfilecache-', 'r-bioc-biocgenerics-', 'r-bioc-biocio-', 'r-bioc-biocparallel-', 'r-bioc-biomart-', 'r-bioc-biostrings-', 'r-bioc-bsgenome-', 'r-bioc-delayedarray-', 'r-bioc-genomeinfodb-', 'r-bioc-genomeinfodbdata-', 'r-bioc-genomicalignments-', 'r-bioc-genomicfeatures-', 'r-bioc-genomicranges-', 'r-bioc-iranges-', 'r-bioc-keggrest-', 'r-bioc-matrixgenerics-', 'r-bioc-rhtslib-', 'r-bioc-rsamtools-', 'r-bioc-rtracklayer-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-summarizedexperiment-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-askpass-', 'r-cran-assertthat-', '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-dbplyr-', 'r-cran-digest-', 'r-cran-dplyr-', 'r-cran-ellipsis-', 'r-cran-fansi-', 'r-cran-fastmap-', 'r-cran-filelock-', 'r-cran-formatr-', 'r-cran-futile.logger-', 'r-cran-futile.options-', 'r-cran-generics-', 'r-cran-glue-', 'r-cran-hms-', 'r-cran-httr-', 'r-cran-jsonlite-', 'r-cran-lambda.r-', 'r-cran-lattice-', 'r-cran-lifecycle-', 'r-cran-littler-', 'r-cran-magrittr-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'r-cran-memoise-', 'r-cran-mime-', 'r-cran-openssl-', 'r-cran-pillar-', 'r-cran-pkgconfig-', 'r-cran-pkgkitten-', 'r-cran-plogr-', 'r-cran-png-', 'r-cran-prettyunits-', 'r-cran-progress-', 'r-cran-purrr-', 'r-cran-r6-', 'r-cran-rappdirs-', 'r-cran-rcpp-', 'r-cran-rcurl-', 'r-cran-restfulr-', 'r-cran-rjson-', 'r-cran-rlang-', 'r-cran-rsqlite-', 'r-cran-snow-', 'r-cran-stringi-', 'r-cran-stringr-', 'r-cran-sys-', 'r-cran-tibble-', 'r-cran-tidyr-', 'r-cran-tidyselect-', 'r-cran-utf8-', 'r-cran-vctrs-', 'r-cran-withr-', 'r-cran-xml-', 'r-cran-xml2-', 'r-cran-yaml-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-variantannotation-'] 2m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'libtirpc3:amd64=1.3.4+ds-1'] 2m50.4s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 3 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/705 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 7507 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2+b1_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2+b1) over (3.9.1-2+b1) ... Preparing to unpack .../libnettle8_3.9.1-2+b1_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2+b1) over (3.9.1-2+b1) ... Setting up libnettle8:amd64 (3.9.1-2+b1) ... Setting up libhogweed6:amd64 (3.9.1-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7511 files and directories currently installed.) Preparing to unpack .../libtirpc3_1.3.4+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.4+ds-1) over (1.3.4+ds-1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-15.1) ... 2m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libhogweed6:amd64=3.9.1-2+b1', 'libnettle8:amd64=3.9.1-2+b1', 'libtirpc3:amd64=1.3.4+ds-1'] 2m50.4s INFO: Running scripts post_remove 2m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_remove_exceptions'] 2m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_remove_exceptions'] 2m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhogweed6t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnettle8t64:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-13-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', '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-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 2m51.1s DUMP: (Reading database ... 7511 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove gcc-11-base which isn't installed dpkg: warning: ignoring request to remove gcc-13-base which isn't installed dpkg: warning: ignoring request to remove libasan6 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-4) ... dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-10-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-13-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libglib2.0-0 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-5) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhogweed6t64 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libnettle8t64 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-3.1) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstdc++-10-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-13-dev which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan0 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for r-base-core (4.3.3-3) ... dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocfilecache which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biomart which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-bsgenome which isn't installed dpkg: warning: ignoring request to remove r-bioc-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicalignments which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicfeatures which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-keggrest which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-dbplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-filelock which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-generics which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-3.1) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 2m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gcc-11-base:amd64', 'gcc-13-base:amd64', 'libasan6:amd64', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgcc-13-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhogweed6t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu67:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnettle8t64:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-10-dev:amd64', 'libstdc++-13-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtiff6:amd64', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', '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-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 2m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', 'r-bioc-variantannotation'] 2m51.1s DUMP: dpkg: warning: ignoring request to remove r-bioc-variantannotation which isn't installed 2m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', 'r-bioc-variantannotation'] 2m51.1s INFO: Running scripts post_purge 2m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_purge_exceptions'] 2m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_purge_exceptions'] 2m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', '--pending'] 2m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--purge', '--pending'] 2m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--remove', '--pending'] 2m51.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg', '--remove', '--pending'] 2m51.1s INFO: Running scripts post_test 2m51.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_test_exceptions'] 2m51.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'tmp/scripts/post_test_exceptions'] 2m51.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m51.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-divert', '--list'] 2m51.5s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 2m51.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'dpkg-divert', '--list'] 2m51.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'clean'] 2m51.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm', 'apt-get', 'clean'] 2m51.6s DEBUG: Recording chroot state 2m52.3s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-mono, fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 2m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/shm'] 2m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/shm'] 2m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/console'] 2m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/console'] 2m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/ptmx'] 2m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/ptmx'] 2m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts'] 2m52.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/dev/pts'] 2m52.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/proc'] 2m52.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm/proc'] 2m52.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m52.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5icx2hzm'] 2m52.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5icx2hzm 2m52.9s INFO: PASS: Upgrading between Debian distributions. 2m52.9s INFO: PASS: All tests. 2m52.9s INFO: piuparts run ends. ret=0 End: 2024-03-17 06:56:29 GMT